Starting phenix.real_space_refine on Thu Sep 26 17:47:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtf_24681/09_2024/7rtf_24681.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtf_24681/09_2024/7rtf_24681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtf_24681/09_2024/7rtf_24681.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtf_24681/09_2024/7rtf_24681.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtf_24681/09_2024/7rtf_24681.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtf_24681/09_2024/7rtf_24681.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 P 8 5.49 5 S 28 5.16 5 C 9052 2.51 5 N 2088 2.21 5 O 2284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13460 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3134 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 24, 'TRANS': 370} Chain breaks: 1 Chain: "A" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 231 Unusual residues: {'PGW': 12} Classifications: {'RNA': 1, 'undetermined': 12} Modifications used: {'rna3p': 1} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 403 Unresolved non-hydrogen angles: 478 Unresolved non-hydrogen dihedrals: 406 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'PGW:plan-1': 10, 'PGW:plan-2': 10, 'PGW:plan-3': 5} Unresolved non-hydrogen planarities: 95 Restraints were copied for chains: C, B, D Time building chain proxies: 7.29, per 1000 atoms: 0.54 Number of scatterers: 13460 At special positions: 0 Unit cell: (105.827, 105.827, 120.01, 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) S 28 16.00 P 8 15.00 O 2284 8.00 N 2088 7.00 C 9052 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.32 Conformation dependent library (CDL) restraints added in 1.6 seconds 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3000 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 8 sheets defined 67.2% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 10 through 36 removed outlier: 3.511A pdb=" N TRP A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) Proline residue: A 31 - end of helix removed outlier: 3.505A pdb=" N VAL A 35 " --> pdb=" O PRO A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 56 removed outlier: 3.539A pdb=" N LEU A 49 " --> pdb=" O PRO A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 63 Processing helix chain 'A' and resid 81 through 87 removed outlier: 3.723A pdb=" N LEU A 85 " --> pdb=" O ARG A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 101 through 106 removed outlier: 3.871A pdb=" N LEU A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 112 removed outlier: 3.962A pdb=" N ARG A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 removed outlier: 3.975A pdb=" N SER A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 158 removed outlier: 3.647A pdb=" N ARG A 136 " --> pdb=" O PRO A 132 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 182 Processing helix chain 'A' and resid 193 through 223 Processing helix chain 'A' and resid 227 through 246 removed outlier: 3.639A pdb=" N TYR A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS A 246 " --> pdb=" O PHE A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 268 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 280 through 292 Processing helix chain 'A' and resid 294 through 299 removed outlier: 3.739A pdb=" N LYS A 298 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 299 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 removed outlier: 3.808A pdb=" N ILE A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 315 " --> pdb=" O ARG A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 4.297A pdb=" N ILE A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 368 through 373' Processing helix chain 'A' and resid 394 through 402 Processing helix chain 'A' and resid 404 through 415 Processing helix chain 'B' and resid 11 through 36 removed outlier: 3.510A pdb=" N TRP B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) Proline residue: B 31 - end of helix removed outlier: 3.506A pdb=" N VAL B 35 " --> pdb=" O PRO B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 56 removed outlier: 3.538A pdb=" N LEU B 49 " --> pdb=" O PRO B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 81 through 87 removed outlier: 3.723A pdb=" N LEU B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 101 through 106 removed outlier: 3.872A pdb=" N LEU B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 112 removed outlier: 3.962A pdb=" N ARG B 111 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 126 removed outlier: 3.974A pdb=" N SER B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 158 removed outlier: 3.647A pdb=" N ARG B 136 " --> pdb=" O PRO B 132 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 182 Processing helix chain 'B' and resid 193 through 223 Processing helix chain 'B' and resid 227 through 246 removed outlier: 3.639A pdb=" N TYR B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 268 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 280 through 292 Processing helix chain 'B' and resid 294 through 299 removed outlier: 3.739A pdb=" N LYS B 298 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 299 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 315 removed outlier: 3.808A pdb=" N ILE B 310 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 removed outlier: 4.297A pdb=" N ILE B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 373 " --> pdb=" O MET B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 373' Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 404 through 415 Processing helix chain 'C' and resid 11 through 36 removed outlier: 3.511A pdb=" N TRP C 18 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE C 28 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Proline residue: C 31 - end of helix removed outlier: 3.505A pdb=" N VAL C 35 " --> pdb=" O PRO C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 56 removed outlier: 3.538A pdb=" N LEU C 49 " --> pdb=" O PRO C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 63 Processing helix chain 'C' and resid 81 through 87 removed outlier: 3.723A pdb=" N LEU C 85 " --> pdb=" O ARG C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'C' and resid 101 through 106 removed outlier: 3.872A pdb=" N LEU C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 removed outlier: 3.961A pdb=" N ARG C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.975A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 158 removed outlier: 3.646A pdb=" N ARG C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU C 137 " --> pdb=" O ALA C 133 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 182 Processing helix chain 'C' and resid 193 through 223 Processing helix chain 'C' and resid 227 through 246 removed outlier: 3.639A pdb=" N TYR C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS C 246 " --> pdb=" O PHE C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 268 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 280 through 292 Processing helix chain 'C' and resid 294 through 299 removed outlier: 3.739A pdb=" N LYS C 298 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C 299 " --> pdb=" O ILE C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 315 removed outlier: 3.808A pdb=" N ILE C 310 " --> pdb=" O GLY C 306 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 4.296A pdb=" N ILE C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU C 373 " --> pdb=" O MET C 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 373' Processing helix chain 'C' and resid 394 through 402 Processing helix chain 'C' and resid 404 through 415 Processing helix chain 'D' and resid 11 through 36 removed outlier: 3.510A pdb=" N TRP D 18 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE D 28 " --> pdb=" O LEU D 24 " (cutoff:3.500A) Proline residue: D 31 - end of helix removed outlier: 3.505A pdb=" N VAL D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 56 removed outlier: 3.538A pdb=" N LEU D 49 " --> pdb=" O PRO D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 63 Processing helix chain 'D' and resid 81 through 87 removed outlier: 3.723A pdb=" N LEU D 85 " --> pdb=" O ARG D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 99 Processing helix chain 'D' and resid 101 through 106 removed outlier: 3.872A pdb=" N LEU D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 112 removed outlier: 3.962A pdb=" N ARG D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 126 removed outlier: 3.974A pdb=" N SER D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 158 removed outlier: 3.646A pdb=" N ARG D 136 " --> pdb=" O PRO D 132 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU D 137 " --> pdb=" O ALA D 133 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 182 Processing helix chain 'D' and resid 193 through 223 Processing helix chain 'D' and resid 227 through 246 removed outlier: 3.640A pdb=" N TYR D 245 " --> pdb=" O ALA D 241 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS D 246 " --> pdb=" O PHE D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 268 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 280 through 292 Processing helix chain 'D' and resid 294 through 299 removed outlier: 3.740A pdb=" N LYS D 298 " --> pdb=" O VAL D 295 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL D 299 " --> pdb=" O ILE D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 315 removed outlier: 3.808A pdb=" N ILE D 310 " --> pdb=" O GLY D 306 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU D 315 " --> pdb=" O ARG D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 removed outlier: 4.297A pdb=" N ILE D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU D 373 " --> pdb=" O MET D 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 368 through 373' Processing helix chain 'D' and resid 394 through 402 Processing helix chain 'D' and resid 404 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 320 Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 329 removed outlier: 6.607A pdb=" N VAL A 381 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 358 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 318 through 320 Processing sheet with id=AA4, first strand: chain 'B' and resid 327 through 329 removed outlier: 6.607A pdb=" N VAL B 381 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B 358 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 318 through 320 Processing sheet with id=AA6, first strand: chain 'C' and resid 327 through 329 removed outlier: 6.607A pdb=" N VAL C 381 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA C 358 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 318 through 320 Processing sheet with id=AA8, first strand: chain 'D' and resid 327 through 329 removed outlier: 6.607A pdb=" N VAL D 381 " --> pdb=" O ILE D 328 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA D 358 " --> pdb=" O VAL D 348 " (cutoff:3.500A) 725 hydrogen bonds defined for protein. 2079 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: 4.67 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3774 1.34 - 1.46: 1908 1.46 - 1.57: 7966 1.57 - 1.69: 12 1.69 - 1.81: 52 Bond restraints: 13712 Sorted by residual: bond pdb=" C10 PGW B 507 " pdb=" C9 PGW B 507 " ideal model delta sigma weight residual 1.333 1.524 -0.191 2.00e-02 2.50e+03 9.10e+01 bond pdb=" C10 PGW C 507 " pdb=" C9 PGW C 507 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.01e+01 bond pdb=" C10 PGW A 507 " pdb=" C9 PGW A 507 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.01e+01 bond pdb=" C10 PGW A 513 " pdb=" C9 PGW A 513 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.00e+01 bond pdb=" C10 PGW D 513 " pdb=" C9 PGW D 513 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 8.98e+01 ... (remaining 13707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 18010 3.44 - 6.88: 330 6.88 - 10.32: 28 10.32 - 13.76: 0 13.76 - 17.21: 48 Bond angle restraints: 18416 Sorted by residual: angle pdb=" C06 PGW C 504 " pdb=" C10 PGW C 504 " pdb=" C9 PGW C 504 " ideal model delta sigma weight residual 126.92 109.71 17.21 3.00e+00 1.11e-01 3.29e+01 angle pdb=" C06 PGW A 504 " pdb=" C10 PGW A 504 " pdb=" C9 PGW A 504 " ideal model delta sigma weight residual 126.92 109.75 17.17 3.00e+00 1.11e-01 3.28e+01 angle pdb=" C06 PGW B 504 " pdb=" C10 PGW B 504 " pdb=" C9 PGW B 504 " ideal model delta sigma weight residual 126.92 109.76 17.16 3.00e+00 1.11e-01 3.27e+01 angle pdb=" C06 PGW D 504 " pdb=" C10 PGW D 504 " pdb=" C9 PGW D 504 " ideal model delta sigma weight residual 126.92 109.77 17.15 3.00e+00 1.11e-01 3.27e+01 angle pdb=" C06 PGW D 509 " pdb=" C10 PGW D 509 " pdb=" C9 PGW D 509 " ideal model delta sigma weight residual 126.92 109.83 17.09 3.00e+00 1.11e-01 3.24e+01 ... (remaining 18411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.49: 7960 33.49 - 66.98: 384 66.98 - 100.46: 32 100.46 - 133.95: 16 133.95 - 167.44: 24 Dihedral angle restraints: 8416 sinusoidal: 3768 harmonic: 4648 Sorted by residual: dihedral pdb=" C5' CMP D 501 " pdb=" O5' CMP D 501 " pdb=" P CMP D 501 " pdb=" O1P CMP D 501 " ideal model delta sinusoidal sigma weight residual 60.00 170.49 -110.49 1 2.00e+01 2.50e-03 3.24e+01 dihedral pdb=" C5' CMP C 501 " pdb=" O5' CMP C 501 " pdb=" P CMP C 501 " pdb=" O1P CMP C 501 " ideal model delta sinusoidal sigma weight residual 60.00 170.46 -110.46 1 2.00e+01 2.50e-03 3.24e+01 dihedral pdb=" C5' CMP A 501 " pdb=" O5' CMP A 501 " pdb=" P CMP A 501 " pdb=" O1P CMP A 501 " ideal model delta sinusoidal sigma weight residual 60.00 170.44 -110.44 1 2.00e+01 2.50e-03 3.24e+01 ... (remaining 8413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1653 0.060 - 0.119: 372 0.119 - 0.179: 83 0.179 - 0.238: 4 0.238 - 0.298: 4 Chirality restraints: 2116 Sorted by residual: chirality pdb=" CB ILE C 58 " pdb=" CA ILE C 58 " pdb=" CG1 ILE C 58 " pdb=" CG2 ILE C 58 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB ILE B 58 " pdb=" CA ILE B 58 " pdb=" CG1 ILE B 58 " pdb=" CG2 ILE B 58 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB ILE A 58 " pdb=" CA ILE A 58 " pdb=" CG1 ILE A 58 " pdb=" CG2 ILE A 58 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 2113 not shown) Planarity restraints: 2212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW A 509 " 0.161 2.00e-02 2.50e+03 1.62e-01 2.64e+02 pdb=" C10 PGW A 509 " -0.155 2.00e-02 2.50e+03 pdb=" C8 PGW A 509 " 0.164 2.00e-02 2.50e+03 pdb=" C9 PGW A 509 " -0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW D 509 " -0.161 2.00e-02 2.50e+03 1.62e-01 2.64e+02 pdb=" C10 PGW D 509 " 0.155 2.00e-02 2.50e+03 pdb=" C8 PGW D 509 " -0.164 2.00e-02 2.50e+03 pdb=" C9 PGW D 509 " 0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW C 509 " -0.161 2.00e-02 2.50e+03 1.62e-01 2.64e+02 pdb=" C10 PGW C 509 " 0.155 2.00e-02 2.50e+03 pdb=" C8 PGW C 509 " -0.164 2.00e-02 2.50e+03 pdb=" C9 PGW C 509 " 0.170 2.00e-02 2.50e+03 ... (remaining 2209 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3207 2.80 - 3.33: 11880 3.33 - 3.85: 20553 3.85 - 4.38: 24240 4.38 - 4.90: 42168 Nonbonded interactions: 102048 Sorted by model distance: nonbonded pdb=" OH TYR A 186 " pdb=" OG1 THR B 180 " model vdw 2.280 3.040 nonbonded pdb=" OH TYR C 186 " pdb=" OG1 THR D 180 " model vdw 2.297 3.040 nonbonded pdb=" OG1 THR A 180 " pdb=" OH TYR D 186 " model vdw 2.304 3.040 nonbonded pdb=" OH TYR B 186 " pdb=" OG1 THR C 180 " model vdw 2.306 3.040 nonbonded pdb=" OH TYR D 327 " pdb=" OE2 GLU D 353 " model vdw 2.307 3.040 ... (remaining 102043 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 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: 0.040 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 31.270 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.030 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:13.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 : 0.009 0.191 13712 Z= 0.588 Angle : 1.363 17.206 18416 Z= 0.553 Chirality : 0.053 0.298 2116 Planarity : 0.013 0.162 2212 Dihedral : 21.044 167.438 5416 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 1.41 % Allowed : 7.94 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.22), residues: 1564 helix: 0.21 (0.18), residues: 952 sheet: -0.45 (0.53), residues: 88 loop : -1.19 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 264 HIS 0.002 0.000 HIS D 316 PHE 0.007 0.001 PHE D 40 TYR 0.013 0.001 TYR D 199 ARG 0.005 0.001 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 1.593 Fit side-chains REVERT: B 334 MET cc_start: 0.7348 (mmp) cc_final: 0.7090 (mmt) REVERT: C 334 MET cc_start: 0.7328 (mmp) cc_final: 0.7063 (mmt) outliers start: 19 outliers final: 4 residues processed: 150 average time/residue: 1.4983 time to fit residues: 243.4533 Evaluate side-chains 145 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 141 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain D residue 314 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.0060 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 47 optimal weight: 0.0030 chunk 74 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 overall best weight: 0.7410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13712 Z= 0.206 Angle : 0.685 10.326 18416 Z= 0.321 Chirality : 0.044 0.185 2116 Planarity : 0.005 0.045 2212 Dihedral : 20.097 159.365 2464 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.11 % Allowed : 12.98 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.22), residues: 1564 helix: 0.88 (0.18), residues: 952 sheet: -0.12 (0.58), residues: 88 loop : -0.99 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 176 HIS 0.002 0.001 HIS B 281 PHE 0.006 0.001 PHE D 366 TYR 0.009 0.001 TYR C 199 ARG 0.007 0.001 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 137 time to evaluate : 1.383 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 138 average time/residue: 1.2474 time to fit residues: 188.8729 Evaluate side-chains 142 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 133 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 314 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 141 optimal weight: 0.8980 chunk 153 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 13712 Z= 0.317 Angle : 0.724 9.422 18416 Z= 0.346 Chirality : 0.047 0.202 2116 Planarity : 0.005 0.046 2212 Dihedral : 18.890 150.643 2464 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.45 % Allowed : 13.20 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.22), residues: 1564 helix: 0.90 (0.18), residues: 960 sheet: 0.11 (0.59), residues: 88 loop : -1.02 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 176 HIS 0.004 0.001 HIS C 149 PHE 0.007 0.002 PHE D 366 TYR 0.011 0.002 TYR A 404 ARG 0.003 0.000 ARG C 254 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 135 time to evaluate : 1.480 Fit side-chains REVERT: A 414 LEU cc_start: 0.4598 (OUTLIER) cc_final: 0.4349 (tm) REVERT: B 414 LEU cc_start: 0.4603 (OUTLIER) cc_final: 0.4365 (tm) REVERT: C 414 LEU cc_start: 0.4611 (OUTLIER) cc_final: 0.4375 (tm) REVERT: D 414 LEU cc_start: 0.4607 (OUTLIER) cc_final: 0.4383 (tm) outliers start: 33 outliers final: 20 residues processed: 154 average time/residue: 1.4595 time to fit residues: 243.4012 Evaluate side-chains 156 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 235 ARG Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 414 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.6980 chunk 106 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 67 optimal weight: 7.9990 chunk 95 optimal weight: 0.3980 chunk 142 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 134 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13712 Z= 0.203 Angle : 0.631 7.993 18416 Z= 0.302 Chirality : 0.044 0.201 2116 Planarity : 0.004 0.041 2212 Dihedral : 17.707 144.771 2464 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.49 % Allowed : 15.36 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.22), residues: 1564 helix: 1.29 (0.18), residues: 952 sheet: 0.08 (0.58), residues: 88 loop : -1.01 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 176 HIS 0.002 0.001 HIS C 292 PHE 0.006 0.001 PHE A 366 TYR 0.015 0.001 TYR D 199 ARG 0.001 0.000 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 134 time to evaluate : 1.503 Fit side-chains REVERT: A 382 ARG cc_start: 0.7765 (mmm160) cc_final: 0.7546 (mmm160) REVERT: B 382 ARG cc_start: 0.7703 (mmm160) cc_final: 0.7491 (mmm160) REVERT: B 414 LEU cc_start: 0.4658 (OUTLIER) cc_final: 0.4445 (tm) REVERT: C 382 ARG cc_start: 0.7766 (mmm160) cc_final: 0.7552 (mmm160) REVERT: C 414 LEU cc_start: 0.4664 (OUTLIER) cc_final: 0.4444 (tm) REVERT: D 382 ARG cc_start: 0.7704 (mmm160) cc_final: 0.7495 (mmm160) REVERT: D 414 LEU cc_start: 0.4686 (OUTLIER) cc_final: 0.4440 (tm) outliers start: 47 outliers final: 15 residues processed: 171 average time/residue: 1.3569 time to fit residues: 252.0532 Evaluate side-chains 151 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 235 ARG Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 414 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 128 optimal weight: 0.2980 chunk 104 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13712 Z= 0.198 Angle : 0.637 10.066 18416 Z= 0.298 Chirality : 0.044 0.213 2116 Planarity : 0.004 0.038 2212 Dihedral : 16.925 137.232 2464 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.60 % Allowed : 17.21 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.22), residues: 1564 helix: 1.44 (0.18), residues: 952 sheet: 0.14 (0.57), residues: 88 loop : -0.89 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 176 HIS 0.002 0.001 HIS C 281 PHE 0.006 0.001 PHE C 366 TYR 0.014 0.001 TYR D 199 ARG 0.003 0.000 ARG B 391 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 146 time to evaluate : 1.459 Fit side-chains REVERT: D 388 ASP cc_start: 0.8082 (t70) cc_final: 0.7740 (t0) outliers start: 35 outliers final: 23 residues processed: 171 average time/residue: 1.3598 time to fit residues: 252.6257 Evaluate side-chains 158 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 235 ARG Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 150 optimal weight: 0.0470 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.6682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13712 Z= 0.184 Angle : 0.630 9.492 18416 Z= 0.294 Chirality : 0.043 0.216 2116 Planarity : 0.004 0.050 2212 Dihedral : 16.249 133.701 2464 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.85 % Allowed : 18.47 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.22), residues: 1564 helix: 1.59 (0.18), residues: 952 sheet: 0.31 (0.57), residues: 88 loop : -0.82 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 176 HIS 0.002 0.001 HIS A 292 PHE 0.006 0.001 PHE D 366 TYR 0.015 0.001 TYR B 199 ARG 0.003 0.000 ARG C 399 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 149 time to evaluate : 1.444 Fit side-chains REVERT: A 388 ASP cc_start: 0.8022 (t70) cc_final: 0.7708 (t0) REVERT: C 388 ASP cc_start: 0.8124 (t70) cc_final: 0.7719 (t0) REVERT: D 388 ASP cc_start: 0.7996 (t70) cc_final: 0.7753 (t0) outliers start: 25 outliers final: 20 residues processed: 168 average time/residue: 1.2631 time to fit residues: 231.6244 Evaluate side-chains 156 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 235 ARG Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 0.0070 chunk 110 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13712 Z= 0.187 Angle : 0.633 10.981 18416 Z= 0.294 Chirality : 0.043 0.221 2116 Planarity : 0.004 0.036 2212 Dihedral : 15.636 133.631 2464 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.60 % Allowed : 17.73 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.22), residues: 1564 helix: 1.72 (0.18), residues: 952 sheet: 0.32 (0.56), residues: 88 loop : -0.74 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 176 HIS 0.002 0.001 HIS A 292 PHE 0.006 0.001 PHE C 366 TYR 0.014 0.001 TYR B 199 ARG 0.005 0.000 ARG C 382 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 149 time to evaluate : 1.508 Fit side-chains REVERT: A 273 ARG cc_start: 0.7996 (mtt-85) cc_final: 0.7778 (mtt90) REVERT: A 384 ARG cc_start: 0.7918 (mtm-85) cc_final: 0.7664 (mtp85) REVERT: A 388 ASP cc_start: 0.7992 (t70) cc_final: 0.7700 (t0) REVERT: B 273 ARG cc_start: 0.7989 (mtt-85) cc_final: 0.7787 (mtt90) REVERT: B 388 ASP cc_start: 0.8108 (t70) cc_final: 0.7757 (t0) REVERT: C 388 ASP cc_start: 0.8065 (t70) cc_final: 0.7681 (t0) outliers start: 35 outliers final: 25 residues processed: 177 average time/residue: 1.0854 time to fit residues: 212.4790 Evaluate side-chains 157 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 132 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 235 ARG Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.8980 chunk 89 optimal weight: 0.0870 chunk 45 optimal weight: 0.9990 chunk 29 optimal weight: 0.0980 chunk 95 optimal weight: 0.5980 chunk 102 optimal weight: 0.2980 chunk 74 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 144 optimal weight: 0.7980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13712 Z= 0.156 Angle : 0.618 12.353 18416 Z= 0.282 Chirality : 0.042 0.230 2116 Planarity : 0.004 0.035 2212 Dihedral : 14.327 133.735 2464 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.45 % Allowed : 18.32 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.23), residues: 1564 helix: 1.90 (0.18), residues: 960 sheet: 0.39 (0.56), residues: 88 loop : -0.73 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 15 HIS 0.001 0.000 HIS A 292 PHE 0.007 0.001 PHE A 40 TYR 0.020 0.001 TYR C 199 ARG 0.003 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 148 time to evaluate : 1.447 Fit side-chains REVERT: A 384 ARG cc_start: 0.7807 (mtm-85) cc_final: 0.7599 (mtp85) REVERT: B 266 THR cc_start: 0.7985 (p) cc_final: 0.7781 (p) REVERT: B 312 ASP cc_start: 0.7755 (m-30) cc_final: 0.7550 (t0) REVERT: B 388 ASP cc_start: 0.7836 (t70) cc_final: 0.7635 (t0) REVERT: C 243 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8029 (mp) REVERT: C 266 THR cc_start: 0.7977 (p) cc_final: 0.7754 (p) outliers start: 33 outliers final: 16 residues processed: 169 average time/residue: 1.2152 time to fit residues: 225.3718 Evaluate side-chains 160 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 143 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 235 ARG Chi-restraints excluded: chain D residue 314 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 chunk 139 optimal weight: 0.4980 chunk 92 optimal weight: 0.0670 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13712 Z= 0.180 Angle : 0.633 12.261 18416 Z= 0.293 Chirality : 0.043 0.229 2116 Planarity : 0.004 0.035 2212 Dihedral : 14.014 133.795 2464 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.93 % Allowed : 18.32 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.23), residues: 1564 helix: 1.96 (0.18), residues: 956 sheet: 0.50 (0.56), residues: 88 loop : -0.71 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 176 HIS 0.002 0.000 HIS C 292 PHE 0.006 0.001 PHE D 366 TYR 0.016 0.001 TYR C 199 ARG 0.004 0.000 ARG C 382 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 150 time to evaluate : 1.503 Fit side-chains REVERT: A 384 ARG cc_start: 0.7802 (mtm-85) cc_final: 0.7576 (mtp85) REVERT: C 243 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7986 (mp) REVERT: C 277 LYS cc_start: 0.8162 (mtmp) cc_final: 0.7860 (mtmt) outliers start: 26 outliers final: 12 residues processed: 162 average time/residue: 1.3122 time to fit residues: 231.4288 Evaluate side-chains 149 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 136 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 235 ARG Chi-restraints excluded: chain D residue 314 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 6.9990 chunk 90 optimal weight: 0.5980 chunk 70 optimal weight: 7.9990 chunk 102 optimal weight: 0.0000 chunk 155 optimal weight: 4.9990 chunk 143 optimal weight: 0.5980 chunk 123 optimal weight: 0.0670 chunk 12 optimal weight: 0.6980 chunk 95 optimal weight: 0.4980 chunk 75 optimal weight: 3.9990 chunk 98 optimal weight: 0.4980 overall best weight: 0.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13712 Z= 0.157 Angle : 0.635 13.078 18416 Z= 0.290 Chirality : 0.042 0.236 2116 Planarity : 0.004 0.034 2212 Dihedral : 13.106 133.678 2464 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.19 % Allowed : 18.84 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.23), residues: 1564 helix: 2.03 (0.18), residues: 948 sheet: 0.48 (0.56), residues: 88 loop : -0.65 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 15 HIS 0.001 0.000 HIS A 292 PHE 0.007 0.001 PHE A 40 TYR 0.020 0.001 TYR C 199 ARG 0.006 0.000 ARG D 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 157 time to evaluate : 1.476 Fit side-chains REVERT: A 311 ARG cc_start: 0.7722 (ttm170) cc_final: 0.7301 (ttm-80) REVERT: A 384 ARG cc_start: 0.7783 (mtm-85) cc_final: 0.7582 (mtp85) REVERT: B 311 ARG cc_start: 0.7793 (ttm170) cc_final: 0.7393 (ttm-80) REVERT: C 243 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7998 (mp) REVERT: D 311 ARG cc_start: 0.7766 (ttm170) cc_final: 0.7324 (ttm-80) outliers start: 16 outliers final: 12 residues processed: 163 average time/residue: 1.3896 time to fit residues: 245.5441 Evaluate side-chains 155 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 142 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 235 ARG Chi-restraints excluded: chain D residue 314 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.9114 > 50: distance: 2 - 19: 11.225 distance: 7 - 26: 34.317 distance: 11 - 31: 25.413 distance: 14 - 19: 11.031 distance: 15 - 42: 26.486 distance: 19 - 20: 20.854 distance: 20 - 21: 20.052 distance: 20 - 23: 17.514 distance: 21 - 26: 8.683 distance: 22 - 50: 27.003 distance: 23 - 24: 22.011 distance: 23 - 25: 21.051 distance: 26 - 27: 29.461 distance: 27 - 28: 13.365 distance: 27 - 30: 11.542 distance: 28 - 29: 30.137 distance: 28 - 31: 14.986 distance: 31 - 32: 13.490 distance: 32 - 33: 7.577 distance: 32 - 35: 29.698 distance: 33 - 34: 9.278 distance: 33 - 42: 9.830 distance: 35 - 36: 14.582 distance: 36 - 37: 27.797 distance: 36 - 38: 11.541 distance: 37 - 39: 21.159 distance: 38 - 40: 9.459 distance: 39 - 41: 29.269 distance: 40 - 41: 17.160 distance: 42 - 43: 44.458 distance: 43 - 44: 5.112 distance: 43 - 46: 51.084 distance: 44 - 50: 20.701 distance: 46 - 47: 30.197 distance: 47 - 48: 4.011 distance: 47 - 49: 24.795 distance: 50 - 51: 9.889 distance: 51 - 52: 15.919 distance: 51 - 54: 18.722 distance: 52 - 53: 41.631 distance: 52 - 56: 43.928 distance: 54 - 55: 26.982 distance: 57 - 58: 36.899 distance: 58 - 59: 34.303 distance: 60 - 61: 26.432 distance: 61 - 62: 31.782 distance: 61 - 63: 15.305 distance: 62 - 64: 39.497 distance: 63 - 65: 49.048 distance: 64 - 66: 18.563 distance: 65 - 66: 9.739 distance: 66 - 67: 15.731 distance: 68 - 69: 25.900 distance: 69 - 70: 42.713 distance: 69 - 72: 14.515 distance: 70 - 71: 24.374 distance: 73 - 74: 40.533 distance: 74 - 75: 18.369 distance: 75 - 76: 44.920 distance: 77 - 78: 29.839 distance: 78 - 79: 26.558 distance: 78 - 81: 20.242 distance: 79 - 80: 29.880 distance: 79 - 88: 32.861 distance: 81 - 82: 26.489 distance: 82 - 83: 26.606 distance: 83 - 84: 12.712 distance: 84 - 85: 17.810 distance: 85 - 86: 9.943 distance: 85 - 87: 32.975 distance: 88 - 89: 19.720 distance: 89 - 90: 38.342 distance: 89 - 92: 43.997 distance: 90 - 91: 38.751 distance: 90 - 96: 39.784 distance: 92 - 94: 41.087 distance: 96 - 97: 6.054 distance: 97 - 98: 11.869 distance: 97 - 100: 43.488 distance: 98 - 99: 22.302 distance: 98 - 102: 27.525 distance: 99 - 123: 30.794 distance: 100 - 101: 17.892