Starting phenix.real_space_refine on Sun May 18 15:14:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ps4_17844/05_2025/8ps4_17844_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ps4_17844/05_2025/8ps4_17844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ps4_17844/05_2025/8ps4_17844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ps4_17844/05_2025/8ps4_17844.map" model { file = "/net/cci-nas-00/data/ceres_data/8ps4_17844/05_2025/8ps4_17844_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ps4_17844/05_2025/8ps4_17844_neut.cif" } resolution = 2.95 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= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5009 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 2 5.21 5 S 40 5.16 5 C 8472 2.51 5 N 2244 2.21 5 O 2452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13210 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3302 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 15, 'TRANS': 388} Chain breaks: 1 Chain: "B" Number of atoms: 3302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3302 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 15, 'TRANS': 388} Chain breaks: 1 Chain: "C" Number of atoms: 3302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3302 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 15, 'TRANS': 388} Chain breaks: 1 Chain: "D" Number of atoms: 3302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3302 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 15, 'TRANS': 388} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.32, per 1000 atoms: 0.71 Number of scatterers: 13210 At special positions: 0 Unit cell: (174.2, 146.25, 73.45, 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 40 16.00 Mg 2 11.99 O 2452 8.00 N 2244 7.00 C 8472 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: 3.43 Conformation dependent library (CDL) restraints added in 1.7 seconds 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3088 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 17 sheets defined 47.1% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 23 through 34 Processing helix chain 'A' and resid 98 through 102 removed outlier: 3.701A pdb=" N PHE A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 98 through 102' Processing helix chain 'A' and resid 110 through 118 Processing helix chain 'A' and resid 135 through 146 Processing helix chain 'A' and resid 150 through 165 Processing helix chain 'A' and resid 173 through 185 removed outlier: 3.686A pdb=" N LYS A 185 " --> pdb=" O TYR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 221 Processing helix chain 'A' and resid 225 through 241 Proline residue: A 235 - end of helix removed outlier: 4.180A pdb=" N THR A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 337 removed outlier: 6.139A pdb=" N VAL A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS A 328 " --> pdb=" O LYS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 382 Processing helix chain 'A' and resid 391 through 408 Processing helix chain 'B' and resid 23 through 34 removed outlier: 3.636A pdb=" N TRP B 27 " --> pdb=" O ILE B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 84 Processing helix chain 'B' and resid 98 through 102 removed outlier: 3.658A pdb=" N PHE B 102 " --> pdb=" O GLU B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 98 through 102' Processing helix chain 'B' and resid 110 through 118 removed outlier: 3.656A pdb=" N LEU B 114 " --> pdb=" O ILE B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 146 Processing helix chain 'B' and resid 148 through 170 Processing helix chain 'B' and resid 171 through 189 Processing helix chain 'B' and resid 195 through 221 Processing helix chain 'B' and resid 225 through 241 Proline residue: B 235 - end of helix removed outlier: 4.017A pdb=" N THR B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 337 removed outlier: 6.044A pdb=" N VAL B 327 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LYS B 328 " --> pdb=" O LYS B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 383 removed outlier: 4.117A pdb=" N TYR B 383 " --> pdb=" O ILE B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 408 Processing helix chain 'C' and resid 22 through 33 Processing helix chain 'C' and resid 98 through 103 removed outlier: 3.648A pdb=" N PHE C 102 " --> pdb=" O GLU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 removed outlier: 3.594A pdb=" N ASN C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 118 Processing helix chain 'C' and resid 135 through 146 Processing helix chain 'C' and resid 148 through 164 removed outlier: 3.550A pdb=" N ILE C 163 " --> pdb=" O ARG C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 removed outlier: 3.664A pdb=" N ASP C 169 " --> pdb=" O ALA C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 185 removed outlier: 3.548A pdb=" N ARG C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS C 185 " --> pdb=" O TYR C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 193 Processing helix chain 'C' and resid 196 through 220 Processing helix chain 'C' and resid 225 through 241 Proline residue: C 235 - end of helix removed outlier: 4.012A pdb=" N THR C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 338 removed outlier: 5.841A pdb=" N VAL C 327 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 381 Processing helix chain 'C' and resid 391 through 408 Processing helix chain 'D' and resid 22 through 34 Processing helix chain 'D' and resid 98 through 102 removed outlier: 3.614A pdb=" N PHE D 102 " --> pdb=" O GLU D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 98 through 102' Processing helix chain 'D' and resid 110 through 118 removed outlier: 3.647A pdb=" N LEU D 114 " --> pdb=" O ILE D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 146 Processing helix chain 'D' and resid 148 through 168 Processing helix chain 'D' and resid 171 through 189 Processing helix chain 'D' and resid 195 through 220 Processing helix chain 'D' and resid 225 through 241 Proline residue: D 235 - end of helix removed outlier: 4.268A pdb=" N THR D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 301 removed outlier: 3.962A pdb=" N ASP D 300 " --> pdb=" O PRO D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 337 removed outlier: 6.058A pdb=" N VAL D 327 " --> pdb=" O SER D 323 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYS D 328 " --> pdb=" O LYS D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 366 Processing helix chain 'D' and resid 369 through 382 Processing helix chain 'D' and resid 391 through 408 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 78 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 104 Processing sheet with id=AA5, first strand: chain 'A' and resid 244 through 255 removed outlier: 6.756A pdb=" N ASP A 269 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LYS A 252 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE A 267 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N PHE A 254 " --> pdb=" O ASN A 265 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN A 265 " --> pdb=" O PHE A 254 " (cutoff:3.500A) removed outlier: 12.015A pdb=" N ILE A 268 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 9.899A pdb=" N VAL A 284 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE A 270 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N ILE A 355 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE A 281 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ILE A 357 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLU A 283 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA A 354 " --> pdb=" O ASP A 388 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N LEU A 390 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE A 356 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 3 through 7 removed outlier: 6.063A pdb=" N VAL B 11 " --> pdb=" O PHE B 68 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 35 through 38 Processing sheet with id=AA8, first strand: chain 'B' and resid 103 through 104 Processing sheet with id=AA9, first strand: chain 'B' and resid 246 through 255 removed outlier: 6.666A pdb=" N ASP B 269 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LYS B 252 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE B 267 " --> pdb=" O LYS B 252 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N PHE B 254 " --> pdb=" O ASN B 265 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASN B 265 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 12.375A pdb=" N ILE B 268 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 10.064A pdb=" N VAL B 284 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE B 270 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA B 354 " --> pdb=" O ASP B 388 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LEU B 390 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ILE B 356 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.549A pdb=" N GLN C 3 " --> pdb=" O THR C 14 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY C 69 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N MET C 13 " --> pdb=" O ASN C 67 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ASN C 67 " --> pdb=" O MET C 13 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N TYR C 15 " --> pdb=" O SER C 65 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N SER C 65 " --> pdb=" O TYR C 15 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N SER C 65 " --> pdb=" O ARG C 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.549A pdb=" N GLN C 3 " --> pdb=" O THR C 14 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY C 69 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N MET C 13 " --> pdb=" O ASN C 67 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ASN C 67 " --> pdb=" O MET C 13 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N TYR C 15 " --> pdb=" O SER C 65 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N SER C 65 " --> pdb=" O TYR C 15 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU C 90 " --> pdb=" O ILE C 126 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 36 through 38 Processing sheet with id=AB4, first strand: chain 'C' and resid 244 through 255 removed outlier: 6.691A pdb=" N ASP C 269 " --> pdb=" O LYS C 250 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LYS C 252 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N PHE C 267 " --> pdb=" O LYS C 252 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N PHE C 254 " --> pdb=" O ASN C 265 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN C 265 " --> pdb=" O PHE C 254 " (cutoff:3.500A) removed outlier: 12.368A pdb=" N ILE C 268 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 10.107A pdb=" N VAL C 284 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE C 270 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASN C 278 " --> pdb=" O ASP C 274 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LEU C 279 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N ILE C 355 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE C 281 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ILE C 357 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLU C 283 " --> pdb=" O ILE C 357 " (cutoff:3.500A) removed outlier: 9.928A pdb=" N ASP C 388 " --> pdb=" O PRO C 352 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA C 354 " --> pdb=" O ASP C 388 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LEU C 390 " --> pdb=" O ALA C 354 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE C 356 " --> pdb=" O LEU C 390 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 3 through 7 removed outlier: 6.765A pdb=" N VAL D 11 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILE D 125 " --> pdb=" O ILE D 134 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 35 through 38 Processing sheet with id=AB7, first strand: chain 'D' and resid 103 through 104 Processing sheet with id=AB8, first strand: chain 'D' and resid 246 through 255 removed outlier: 6.737A pdb=" N ASP D 269 " --> pdb=" O LYS D 250 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LYS D 252 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N PHE D 267 " --> pdb=" O LYS D 252 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N PHE D 254 " --> pdb=" O ASN D 265 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ASN D 265 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 12.557A pdb=" N ILE D 268 " --> pdb=" O VAL D 284 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N VAL D 284 " --> pdb=" O ILE D 268 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE D 270 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA D 354 " --> pdb=" O ASP D 388 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N LEU D 390 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ILE D 356 " --> pdb=" O LEU D 390 " (cutoff:3.500A) 668 hydrogen bonds defined for protein. 1893 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: 3.99 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2680 1.33 - 1.45: 2969 1.45 - 1.57: 7739 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 13460 Sorted by residual: bond pdb=" N ILE C 134 " pdb=" CA ILE C 134 " ideal model delta sigma weight residual 1.460 1.493 -0.033 7.50e-03 1.78e+04 1.95e+01 bond pdb=" N ILE B 41 " pdb=" CA ILE B 41 " ideal model delta sigma weight residual 1.456 1.494 -0.038 9.50e-03 1.11e+04 1.58e+01 bond pdb=" N ILE C 41 " pdb=" CA ILE C 41 " ideal model delta sigma weight residual 1.456 1.494 -0.038 9.50e-03 1.11e+04 1.58e+01 bond pdb=" N ILE A 41 " pdb=" CA ILE A 41 " ideal model delta sigma weight residual 1.459 1.495 -0.036 9.10e-03 1.21e+04 1.57e+01 bond pdb=" N ILE A 303 " pdb=" CA ILE A 303 " ideal model delta sigma weight residual 1.462 1.494 -0.032 8.70e-03 1.32e+04 1.37e+01 ... (remaining 13455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 14137 1.89 - 3.78: 3866 3.78 - 5.67: 162 5.67 - 7.56: 13 7.56 - 9.45: 2 Bond angle restraints: 18180 Sorted by residual: angle pdb=" N ILE C 292 " pdb=" CA ILE C 292 " pdb=" C ILE C 292 " ideal model delta sigma weight residual 112.90 105.89 7.01 9.60e-01 1.09e+00 5.33e+01 angle pdb=" N ILE C 234 " pdb=" CA ILE C 234 " pdb=" CB ILE C 234 " ideal model delta sigma weight residual 110.50 114.50 -4.00 6.30e-01 2.52e+00 4.04e+01 angle pdb=" N ILE D 292 " pdb=" CA ILE D 292 " pdb=" C ILE D 292 " ideal model delta sigma weight residual 113.22 106.87 6.35 1.23e+00 6.61e-01 2.66e+01 angle pdb=" N THR A 222 " pdb=" CA THR A 222 " pdb=" C THR A 222 " ideal model delta sigma weight residual 114.31 107.73 6.58 1.29e+00 6.01e-01 2.61e+01 angle pdb=" N LYS D 190 " pdb=" CA LYS D 190 " pdb=" C LYS D 190 " ideal model delta sigma weight residual 113.97 107.67 6.30 1.28e+00 6.10e-01 2.42e+01 ... (remaining 18175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 7559 17.35 - 34.70: 537 34.70 - 52.04: 105 52.04 - 69.39: 16 69.39 - 86.74: 7 Dihedral angle restraints: 8224 sinusoidal: 3456 harmonic: 4768 Sorted by residual: dihedral pdb=" C GLN B 362 " pdb=" N GLN B 362 " pdb=" CA GLN B 362 " pdb=" CB GLN B 362 " ideal model delta harmonic sigma weight residual -122.60 -135.96 13.36 0 2.50e+00 1.60e-01 2.86e+01 dihedral pdb=" C ASN B 73 " pdb=" N ASN B 73 " pdb=" CA ASN B 73 " pdb=" CB ASN B 73 " ideal model delta harmonic sigma weight residual -122.60 -134.15 11.55 0 2.50e+00 1.60e-01 2.13e+01 dihedral pdb=" C ASN C 365 " pdb=" N ASN C 365 " pdb=" CA ASN C 365 " pdb=" CB ASN C 365 " ideal model delta harmonic sigma weight residual -122.60 -133.65 11.05 0 2.50e+00 1.60e-01 1.95e+01 ... (remaining 8221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 953 0.081 - 0.162: 806 0.162 - 0.243: 250 0.243 - 0.324: 24 0.324 - 0.405: 3 Chirality restraints: 2036 Sorted by residual: chirality pdb=" CA GLN B 362 " pdb=" N GLN B 362 " pdb=" C GLN B 362 " pdb=" CB GLN B 362 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CA ASN B 73 " pdb=" N ASN B 73 " pdb=" C ASN B 73 " pdb=" CB ASN B 73 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA ASN C 365 " pdb=" N ASN C 365 " pdb=" C ASN C 365 " pdb=" CB ASN C 365 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 2033 not shown) Planarity restraints: 2328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 58 " 0.021 2.00e-02 2.50e+03 4.35e-02 1.90e+01 pdb=" C ASP D 58 " -0.075 2.00e-02 2.50e+03 pdb=" O ASP D 58 " 0.028 2.00e-02 2.50e+03 pdb=" N PHE D 59 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 59 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.25e+00 pdb=" C PHE D 59 " 0.043 2.00e-02 2.50e+03 pdb=" O PHE D 59 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN D 60 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 381 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C ARG C 381 " -0.039 2.00e-02 2.50e+03 pdb=" O ARG C 381 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS C 382 " 0.013 2.00e-02 2.50e+03 ... (remaining 2325 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 3940 2.84 - 3.35: 12596 3.35 - 3.87: 22223 3.87 - 4.38: 26581 4.38 - 4.90: 43464 Nonbonded interactions: 108804 Sorted by model distance: nonbonded pdb=" O ASP D 58 " pdb=" C PHE D 59 " model vdw 2.319 3.270 nonbonded pdb=" O ASN A 276 " pdb=" NH2 ARG A 348 " model vdw 2.452 3.120 nonbonded pdb=" O VAL A 7 " pdb=" OD1 ASP A 10 " model vdw 2.478 3.040 nonbonded pdb=" N THR B 391 " pdb=" O THR B 391 " model vdw 2.508 2.496 nonbonded pdb=" N THR C 391 " pdb=" O THR C 391 " model vdw 2.525 2.496 ... (remaining 108799 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 408) selection = chain 'C' selection = (chain 'D' and resid 1 through 408) } 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: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 0.730 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 33.500 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 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:10.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 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 : 0.012 0.040 13460 Z= 0.949 Angle : 1.464 9.448 18180 Z= 1.169 Chirality : 0.110 0.405 2036 Planarity : 0.004 0.044 2328 Dihedral : 12.309 86.741 5136 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.97 % Allowed : 5.98 % Favored : 92.05 % Cbeta Deviations : 0.26 % 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: 3.21 (0.22), residues: 1600 helix: 4.17 (0.18), residues: 704 sheet: 1.28 (0.38), residues: 216 loop : 0.16 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 325 HIS 0.004 0.001 HIS D 161 PHE 0.013 0.002 PHE D 111 TYR 0.016 0.002 TYR B 392 ARG 0.004 0.000 ARG C 154 Details of bonding type rmsd hydrogen bonds : bond 0.16370 ( 662) hydrogen bonds : angle 6.81739 ( 1893) covalent geometry : bond 0.01218 (13460) covalent geometry : angle 1.46367 (18180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 214 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 PHE cc_start: 0.7230 (m-80) cc_final: 0.6870 (m-80) REVERT: B 106 ARG cc_start: 0.7733 (mmm160) cc_final: 0.7476 (mmm160) REVERT: B 171 MET cc_start: 0.7581 (mtm) cc_final: 0.7243 (pmm) REVERT: C 68 PHE cc_start: 0.7763 (t80) cc_final: 0.7194 (t80) REVERT: C 130 LYS cc_start: 0.7839 (mmmt) cc_final: 0.7139 (mptt) REVERT: D 276 ASN cc_start: 0.7833 (m110) cc_final: 0.7543 (m110) outliers start: 29 outliers final: 0 residues processed: 238 average time/residue: 1.2641 time to fit residues: 327.5839 Evaluate side-chains 99 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 41 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN B 148 ASN B 265 ASN B 276 ASN B 365 ASN C 143 GLN D 230 GLN D 372 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.156325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.101088 restraints weight = 18769.907| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.66 r_work: 0.3307 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13460 Z= 0.138 Angle : 0.513 6.256 18180 Z= 0.284 Chirality : 0.043 0.196 2036 Planarity : 0.003 0.032 2328 Dihedral : 3.884 17.570 1768 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 1.56 % Allowed : 12.64 % Favored : 85.80 % 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: 2.78 (0.21), residues: 1600 helix: 3.54 (0.18), residues: 704 sheet: 1.08 (0.39), residues: 206 loop : 0.29 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 325 HIS 0.004 0.001 HIS D 321 PHE 0.017 0.001 PHE A 376 TYR 0.014 0.001 TYR A 167 ARG 0.004 0.000 ARG D 87 Details of bonding type rmsd hydrogen bonds : bond 0.04395 ( 662) hydrogen bonds : angle 5.12132 ( 1893) covalent geometry : bond 0.00313 (13460) covalent geometry : angle 0.51317 (18180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 1.452 Fit side-chains revert: symmetry clash REVERT: A 134 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7493 (mm) REVERT: B 72 ASN cc_start: 0.7055 (m110) cc_final: 0.6716 (m-40) REVERT: B 100 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.6708 (tptm) REVERT: B 106 ARG cc_start: 0.8027 (mmm160) cc_final: 0.7648 (mmm160) REVERT: B 189 ARG cc_start: 0.8190 (mtp85) cc_final: 0.7935 (ttt90) REVERT: B 305 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8178 (p) REVERT: C 1 MET cc_start: 0.6098 (pp-130) cc_final: 0.5771 (pp-130) REVERT: C 68 PHE cc_start: 0.7993 (t80) cc_final: 0.7281 (t80) REVERT: C 130 LYS cc_start: 0.7939 (mmmt) cc_final: 0.7481 (mptt) REVERT: C 216 ASP cc_start: 0.7757 (m-30) cc_final: 0.7349 (OUTLIER) REVERT: D 23 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7351 (tt) REVERT: D 79 PRO cc_start: 0.8382 (Cg_exo) cc_final: 0.8150 (Cg_endo) REVERT: D 177 ARG cc_start: 0.7750 (mmt90) cc_final: 0.7079 (mmm160) outliers start: 23 outliers final: 4 residues processed: 131 average time/residue: 1.0973 time to fit residues: 159.4158 Evaluate side-chains 98 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 168 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 97 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 120 optimal weight: 20.0000 chunk 125 optimal weight: 30.0000 chunk 11 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 65 optimal weight: 0.0370 overall best weight: 1.5062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN B 385 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.150255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.092842 restraints weight = 19039.002| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.70 r_work: 0.3169 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13460 Z= 0.161 Angle : 0.504 7.438 18180 Z= 0.276 Chirality : 0.044 0.182 2036 Planarity : 0.003 0.035 2328 Dihedral : 3.908 18.486 1768 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.83 % Allowed : 13.45 % Favored : 84.71 % 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: 2.47 (0.21), residues: 1600 helix: 3.28 (0.18), residues: 684 sheet: 0.82 (0.38), residues: 216 loop : 0.27 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 229 HIS 0.008 0.001 HIS B 321 PHE 0.016 0.001 PHE A 376 TYR 0.012 0.001 TYR C 167 ARG 0.005 0.000 ARG C 154 Details of bonding type rmsd hydrogen bonds : bond 0.04091 ( 662) hydrogen bonds : angle 4.76221 ( 1893) covalent geometry : bond 0.00383 (13460) covalent geometry : angle 0.50438 (18180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 1.455 Fit side-chains revert: symmetry clash REVERT: A 136 LYS cc_start: 0.7886 (ttpp) cc_final: 0.7484 (tttp) REVERT: A 202 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7897 (mt) REVERT: B 72 ASN cc_start: 0.7210 (m110) cc_final: 0.6952 (m-40) REVERT: B 106 ARG cc_start: 0.8157 (mmm160) cc_final: 0.7755 (mmm160) REVERT: B 195 ASP cc_start: 0.7597 (t0) cc_final: 0.7392 (t0) REVERT: B 305 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8332 (p) REVERT: C 1 MET cc_start: 0.6009 (pp-130) cc_final: 0.5663 (pp-130) REVERT: C 68 PHE cc_start: 0.7899 (t80) cc_final: 0.7174 (t80) REVERT: C 130 LYS cc_start: 0.7947 (mmmt) cc_final: 0.7494 (mptt) REVERT: C 202 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7992 (mt) REVERT: C 216 ASP cc_start: 0.7860 (m-30) cc_final: 0.7417 (OUTLIER) REVERT: C 286 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8082 (mmtm) REVERT: D 23 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7379 (tt) REVERT: D 68 PHE cc_start: 0.7305 (t80) cc_final: 0.7105 (t80) REVERT: D 79 PRO cc_start: 0.8568 (Cg_exo) cc_final: 0.8272 (Cg_endo) REVERT: D 177 ARG cc_start: 0.7922 (mmt90) cc_final: 0.7112 (mmm160) REVERT: D 226 GLU cc_start: 0.8283 (tt0) cc_final: 0.8058 (tt0) outliers start: 27 outliers final: 4 residues processed: 128 average time/residue: 1.0761 time to fit residues: 153.4120 Evaluate side-chains 101 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 168 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 36 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 124 optimal weight: 0.2980 chunk 115 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 GLN A 365 ASN B 92 HIS B 362 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.149068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.091313 restraints weight = 18881.435| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.71 r_work: 0.3143 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13460 Z= 0.153 Angle : 0.482 7.247 18180 Z= 0.262 Chirality : 0.043 0.183 2036 Planarity : 0.003 0.035 2328 Dihedral : 3.859 19.195 1768 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.70 % Allowed : 14.47 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.21), residues: 1600 helix: 3.14 (0.18), residues: 686 sheet: 0.56 (0.37), residues: 216 loop : 0.22 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 27 HIS 0.003 0.001 HIS D 161 PHE 0.014 0.001 PHE A 376 TYR 0.011 0.001 TYR A 392 ARG 0.004 0.000 ARG C 154 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 662) hydrogen bonds : angle 4.62263 ( 1893) covalent geometry : bond 0.00368 (13460) covalent geometry : angle 0.48248 (18180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7887 (mt) REVERT: B 72 ASN cc_start: 0.7343 (m110) cc_final: 0.7081 (m-40) REVERT: B 305 THR cc_start: 0.8567 (OUTLIER) cc_final: 0.8323 (p) REVERT: C 1 MET cc_start: 0.6052 (pp-130) cc_final: 0.5697 (pp-130) REVERT: C 4 PHE cc_start: 0.7397 (m-80) cc_final: 0.6979 (m-80) REVERT: C 68 PHE cc_start: 0.7921 (t80) cc_final: 0.7195 (t80) REVERT: C 130 LYS cc_start: 0.8018 (mmmt) cc_final: 0.7559 (mptt) REVERT: C 202 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7951 (mt) REVERT: C 216 ASP cc_start: 0.7844 (m-30) cc_final: 0.7399 (OUTLIER) REVERT: C 286 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8056 (mmtm) REVERT: D 79 PRO cc_start: 0.8512 (Cg_exo) cc_final: 0.8286 (Cg_endo) REVERT: D 100 LYS cc_start: 0.7693 (mtmm) cc_final: 0.7189 (ptmt) REVERT: D 193 LYS cc_start: 0.8569 (tppp) cc_final: 0.8234 (tptt) outliers start: 25 outliers final: 6 residues processed: 116 average time/residue: 1.0265 time to fit residues: 133.6428 Evaluate side-chains 97 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 387 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 78 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 chunk 120 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN B 362 GLN D 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.149863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.092429 restraints weight = 19003.919| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.71 r_work: 0.3160 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13460 Z= 0.116 Angle : 0.457 6.731 18180 Z= 0.248 Chirality : 0.042 0.176 2036 Planarity : 0.003 0.028 2328 Dihedral : 3.768 19.207 1768 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.56 % Allowed : 15.42 % Favored : 83.02 % 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: 2.34 (0.21), residues: 1600 helix: 3.21 (0.18), residues: 686 sheet: 0.52 (0.37), residues: 216 loop : 0.22 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 27 HIS 0.002 0.001 HIS B 161 PHE 0.013 0.001 PHE A 376 TYR 0.011 0.001 TYR A 167 ARG 0.003 0.000 ARG C 154 Details of bonding type rmsd hydrogen bonds : bond 0.03468 ( 662) hydrogen bonds : angle 4.51115 ( 1893) covalent geometry : bond 0.00266 (13460) covalent geometry : angle 0.45738 (18180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 1.656 Fit side-chains revert: symmetry clash REVERT: A 136 LYS cc_start: 0.7892 (ttpp) cc_final: 0.7504 (tttp) REVERT: A 202 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7861 (mt) REVERT: B 72 ASN cc_start: 0.7390 (m110) cc_final: 0.7153 (m-40) REVERT: B 190 LYS cc_start: 0.8447 (mtmm) cc_final: 0.8083 (mttm) REVERT: B 305 THR cc_start: 0.8568 (OUTLIER) cc_final: 0.8330 (p) REVERT: B 362 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7859 (pm20) REVERT: C 1 MET cc_start: 0.6065 (pp-130) cc_final: 0.5695 (pp-130) REVERT: C 68 PHE cc_start: 0.7901 (t80) cc_final: 0.7085 (t80) REVERT: C 130 LYS cc_start: 0.8011 (mmmt) cc_final: 0.7618 (mptt) REVERT: C 202 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7964 (mt) REVERT: C 216 ASP cc_start: 0.7828 (m-30) cc_final: 0.7390 (OUTLIER) REVERT: C 286 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.8016 (mmtm) REVERT: D 23 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7546 (tt) REVERT: D 79 PRO cc_start: 0.8510 (Cg_exo) cc_final: 0.8278 (Cg_endo) REVERT: D 100 LYS cc_start: 0.7697 (mtmm) cc_final: 0.7183 (ptmt) REVERT: D 106 ARG cc_start: 0.8472 (mmp-170) cc_final: 0.7866 (mmp80) REVERT: D 193 LYS cc_start: 0.8527 (tppp) cc_final: 0.8171 (tptt) outliers start: 23 outliers final: 10 residues processed: 113 average time/residue: 1.0484 time to fit residues: 133.2390 Evaluate side-chains 99 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 168 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 47 optimal weight: 20.0000 chunk 32 optimal weight: 0.8980 chunk 87 optimal weight: 20.0000 chunk 142 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 = 0.4064 r_free = 0.4064 target = 0.151801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.093281 restraints weight = 18962.695| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.75 r_work: 0.3137 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13460 Z= 0.172 Angle : 0.487 7.497 18180 Z= 0.262 Chirality : 0.043 0.183 2036 Planarity : 0.003 0.055 2328 Dihedral : 3.822 19.988 1768 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.97 % Allowed : 15.01 % Favored : 83.02 % 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: 2.24 (0.21), residues: 1600 helix: 3.08 (0.18), residues: 684 sheet: 0.45 (0.37), residues: 212 loop : 0.24 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 27 HIS 0.003 0.001 HIS D 321 PHE 0.034 0.001 PHE C 111 TYR 0.010 0.001 TYR B 392 ARG 0.010 0.000 ARG A 87 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 662) hydrogen bonds : angle 4.52600 ( 1893) covalent geometry : bond 0.00421 (13460) covalent geometry : angle 0.48667 (18180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 90 time to evaluate : 1.529 Fit side-chains revert: symmetry clash REVERT: A 136 LYS cc_start: 0.7946 (ttpp) cc_final: 0.7587 (tttp) REVERT: A 190 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8963 (mmmt) REVERT: A 202 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7849 (mt) REVERT: B 72 ASN cc_start: 0.7440 (m110) cc_final: 0.7205 (m-40) REVERT: B 305 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8278 (p) REVERT: B 362 GLN cc_start: 0.8188 (pp30) cc_final: 0.7210 (pp30) REVERT: B 388 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.8572 (t0) REVERT: C 1 MET cc_start: 0.6020 (pp-130) cc_final: 0.5622 (pp-130) REVERT: C 68 PHE cc_start: 0.7840 (t80) cc_final: 0.7061 (t80) REVERT: C 79 PRO cc_start: 0.8502 (Cg_exo) cc_final: 0.8286 (Cg_endo) REVERT: C 130 LYS cc_start: 0.8044 (mmmt) cc_final: 0.7451 (mptt) REVERT: C 202 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7963 (mt) REVERT: C 216 ASP cc_start: 0.7815 (m-30) cc_final: 0.7377 (t70) REVERT: C 286 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8182 (mmtm) REVERT: D 23 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7539 (tt) REVERT: D 79 PRO cc_start: 0.8545 (Cg_exo) cc_final: 0.8309 (Cg_endo) REVERT: D 100 LYS cc_start: 0.7730 (mtmm) cc_final: 0.7206 (ptmt) REVERT: D 106 ARG cc_start: 0.8447 (mmp-170) cc_final: 0.7816 (mmp80) REVERT: D 171 MET cc_start: 0.7561 (mmt) cc_final: 0.7283 (mmt) REVERT: D 193 LYS cc_start: 0.8567 (tppp) cc_final: 0.8220 (tptt) outliers start: 29 outliers final: 9 residues processed: 111 average time/residue: 1.0757 time to fit residues: 133.1074 Evaluate side-chains 102 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 168 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 87 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 124 optimal weight: 0.0070 chunk 71 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 144 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 147 optimal weight: 0.6980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.149398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.094356 restraints weight = 18054.314| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.59 r_work: 0.3181 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13460 Z= 0.101 Angle : 0.442 8.613 18180 Z= 0.238 Chirality : 0.041 0.180 2036 Planarity : 0.003 0.044 2328 Dihedral : 3.668 20.059 1768 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.90 % Allowed : 15.42 % Favored : 82.68 % 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: 2.32 (0.21), residues: 1600 helix: 3.24 (0.18), residues: 686 sheet: 0.55 (0.38), residues: 212 loop : 0.16 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 27 HIS 0.002 0.000 HIS D 161 PHE 0.012 0.001 PHE A 376 TYR 0.012 0.001 TYR D 392 ARG 0.008 0.000 ARG A 87 Details of bonding type rmsd hydrogen bonds : bond 0.03181 ( 662) hydrogen bonds : angle 4.36818 ( 1893) covalent geometry : bond 0.00224 (13460) covalent geometry : angle 0.44154 (18180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 1.649 Fit side-chains revert: symmetry clash REVERT: A 136 LYS cc_start: 0.7950 (ttpp) cc_final: 0.7602 (tttp) REVERT: A 202 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7875 (mt) REVERT: B 72 ASN cc_start: 0.7491 (m110) cc_final: 0.7271 (m-40) REVERT: B 129 ASP cc_start: 0.8615 (p0) cc_final: 0.8034 (m-30) REVERT: B 305 THR cc_start: 0.8566 (OUTLIER) cc_final: 0.8347 (p) REVERT: B 313 MET cc_start: 0.8563 (tpp) cc_final: 0.8271 (mmm) REVERT: C 1 MET cc_start: 0.6013 (pp-130) cc_final: 0.5605 (pp-130) REVERT: C 4 PHE cc_start: 0.7358 (m-80) cc_final: 0.6433 (m-80) REVERT: C 68 PHE cc_start: 0.7857 (t80) cc_final: 0.6979 (t80) REVERT: C 130 LYS cc_start: 0.8070 (mmmt) cc_final: 0.7570 (mptt) REVERT: C 202 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7957 (mt) REVERT: C 216 ASP cc_start: 0.7821 (m-30) cc_final: 0.7397 (t70) REVERT: C 286 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8058 (mmtm) REVERT: D 23 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7568 (tt) REVERT: D 79 PRO cc_start: 0.8560 (Cg_exo) cc_final: 0.8327 (Cg_endo) REVERT: D 100 LYS cc_start: 0.7730 (mtmm) cc_final: 0.7225 (ptmt) REVERT: D 106 ARG cc_start: 0.8391 (mmp-170) cc_final: 0.7724 (mmp80) REVERT: D 193 LYS cc_start: 0.8532 (tppp) cc_final: 0.8192 (tptt) outliers start: 28 outliers final: 8 residues processed: 114 average time/residue: 1.0447 time to fit residues: 133.9766 Evaluate side-chains 100 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 168 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 159 optimal weight: 0.6980 chunk 110 optimal weight: 0.7980 chunk 136 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 20.0000 chunk 76 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.149156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.091760 restraints weight = 18748.506| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.63 r_work: 0.3123 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 13460 Z= 0.199 Angle : 0.502 8.657 18180 Z= 0.269 Chirality : 0.044 0.176 2036 Planarity : 0.003 0.041 2328 Dihedral : 3.822 20.291 1768 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.70 % Allowed : 15.90 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.15 (0.21), residues: 1600 helix: 3.01 (0.18), residues: 686 sheet: 0.41 (0.37), residues: 212 loop : 0.19 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 27 HIS 0.003 0.001 HIS D 92 PHE 0.013 0.001 PHE C 376 TYR 0.010 0.001 TYR B 392 ARG 0.007 0.000 ARG A 87 Details of bonding type rmsd hydrogen bonds : bond 0.03903 ( 662) hydrogen bonds : angle 4.48420 ( 1893) covalent geometry : bond 0.00491 (13460) covalent geometry : angle 0.50231 (18180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 1.696 Fit side-chains revert: symmetry clash REVERT: A 136 LYS cc_start: 0.8010 (ttpp) cc_final: 0.7643 (tttp) REVERT: A 202 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7931 (mt) REVERT: B 129 ASP cc_start: 0.8615 (p0) cc_final: 0.8050 (m-30) REVERT: B 293 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7774 (mp) REVERT: B 305 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8316 (p) REVERT: C 1 MET cc_start: 0.6105 (pp-130) cc_final: 0.5643 (pp-130) REVERT: C 68 PHE cc_start: 0.7844 (t80) cc_final: 0.7056 (t80) REVERT: C 130 LYS cc_start: 0.8089 (mmmt) cc_final: 0.7595 (mptt) REVERT: C 202 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7991 (mt) REVERT: C 216 ASP cc_start: 0.7824 (m-30) cc_final: 0.7408 (t70) REVERT: C 286 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8217 (mmtp) REVERT: C 294 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7730 (mtt-85) REVERT: D 23 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7559 (tt) REVERT: D 79 PRO cc_start: 0.8626 (Cg_exo) cc_final: 0.8393 (Cg_endo) REVERT: D 100 LYS cc_start: 0.7825 (mtmm) cc_final: 0.7295 (ptmt) REVERT: D 106 ARG cc_start: 0.8409 (mmp-170) cc_final: 0.7734 (mmp80) REVERT: D 193 LYS cc_start: 0.8579 (tppp) cc_final: 0.8258 (tptt) outliers start: 25 outliers final: 6 residues processed: 108 average time/residue: 1.0700 time to fit residues: 129.3932 Evaluate side-chains 101 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain C residue 294 ARG Chi-restraints excluded: chain D residue 23 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 2.9990 chunk 7 optimal weight: 0.0770 chunk 156 optimal weight: 1.9990 chunk 40 optimal weight: 20.0000 chunk 152 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.148551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.090818 restraints weight = 18334.925| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.67 r_work: 0.3130 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13460 Z= 0.157 Angle : 0.484 9.148 18180 Z= 0.259 Chirality : 0.043 0.174 2036 Planarity : 0.003 0.042 2328 Dihedral : 3.812 20.559 1768 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.29 % Allowed : 16.30 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.15 (0.21), residues: 1600 helix: 3.01 (0.18), residues: 686 sheet: 0.39 (0.37), residues: 212 loop : 0.20 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 27 HIS 0.002 0.001 HIS D 92 PHE 0.012 0.001 PHE C 4 TYR 0.014 0.001 TYR A 167 ARG 0.006 0.000 ARG A 87 Details of bonding type rmsd hydrogen bonds : bond 0.03642 ( 662) hydrogen bonds : angle 4.43930 ( 1893) covalent geometry : bond 0.00382 (13460) covalent geometry : angle 0.48405 (18180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 1.499 Fit side-chains revert: symmetry clash REVERT: A 136 LYS cc_start: 0.8007 (ttpp) cc_final: 0.7626 (tttp) REVERT: A 202 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7951 (mt) REVERT: B 129 ASP cc_start: 0.8613 (p0) cc_final: 0.8111 (m-30) REVERT: B 293 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7827 (mp) REVERT: B 305 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8320 (p) REVERT: C 1 MET cc_start: 0.6072 (pp-130) cc_final: 0.5616 (pp-130) REVERT: C 4 PHE cc_start: 0.7254 (m-80) cc_final: 0.6497 (m-10) REVERT: C 68 PHE cc_start: 0.7840 (t80) cc_final: 0.7027 (t80) REVERT: C 130 LYS cc_start: 0.8104 (mmmt) cc_final: 0.7691 (mptt) REVERT: C 202 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7992 (mt) REVERT: C 216 ASP cc_start: 0.7839 (m-30) cc_final: 0.7414 (t70) REVERT: D 23 ILE cc_start: 0.8266 (OUTLIER) cc_final: 0.7579 (tt) REVERT: D 100 LYS cc_start: 0.7824 (mtmm) cc_final: 0.7306 (ptmt) REVERT: D 106 ARG cc_start: 0.8418 (mmp-170) cc_final: 0.7662 (mmp80) REVERT: D 193 LYS cc_start: 0.8593 (tppp) cc_final: 0.8275 (tptt) REVERT: D 313 MET cc_start: 0.8597 (tpp) cc_final: 0.8267 (mmm) outliers start: 19 outliers final: 5 residues processed: 102 average time/residue: 1.0954 time to fit residues: 125.0350 Evaluate side-chains 94 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 23 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 127 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.149561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.092358 restraints weight = 18419.179| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.84 r_work: 0.3136 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13460 Z= 0.120 Angle : 0.470 9.608 18180 Z= 0.250 Chirality : 0.041 0.173 2036 Planarity : 0.003 0.042 2328 Dihedral : 3.722 20.418 1768 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.95 % Allowed : 16.78 % Favored : 82.27 % 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: 2.26 (0.21), residues: 1600 helix: 3.13 (0.18), residues: 686 sheet: 0.43 (0.38), residues: 212 loop : 0.21 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 27 HIS 0.002 0.001 HIS D 161 PHE 0.012 0.001 PHE C 4 TYR 0.011 0.001 TYR D 392 ARG 0.007 0.000 ARG A 87 Details of bonding type rmsd hydrogen bonds : bond 0.03349 ( 662) hydrogen bonds : angle 4.34543 ( 1893) covalent geometry : bond 0.00277 (13460) covalent geometry : angle 0.46968 (18180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 1.680 Fit side-chains revert: symmetry clash REVERT: A 136 LYS cc_start: 0.8042 (ttpp) cc_final: 0.7674 (tttp) REVERT: A 202 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7773 (mt) REVERT: B 68 PHE cc_start: 0.8543 (t80) cc_final: 0.7966 (t80) REVERT: B 129 ASP cc_start: 0.8503 (p0) cc_final: 0.8012 (m-30) REVERT: B 293 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7616 (mp) REVERT: B 305 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8233 (p) REVERT: B 313 MET cc_start: 0.8471 (tpp) cc_final: 0.8148 (mmm) REVERT: C 4 PHE cc_start: 0.7194 (m-80) cc_final: 0.6520 (m-10) REVERT: C 68 PHE cc_start: 0.7837 (t80) cc_final: 0.7176 (t80) REVERT: C 130 LYS cc_start: 0.8128 (mmmt) cc_final: 0.7737 (mptt) REVERT: C 202 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7871 (mt) REVERT: C 216 ASP cc_start: 0.7707 (m-30) cc_final: 0.7356 (t70) REVERT: D 23 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.7595 (tt) REVERT: D 100 LYS cc_start: 0.7825 (mtmm) cc_final: 0.7325 (ptmt) REVERT: D 106 ARG cc_start: 0.8382 (mmp-170) cc_final: 0.7619 (mmp80) REVERT: D 193 LYS cc_start: 0.8547 (tppp) cc_final: 0.8247 (tptt) outliers start: 14 outliers final: 5 residues processed: 102 average time/residue: 1.0486 time to fit residues: 120.2647 Evaluate side-chains 94 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 23 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 126 optimal weight: 0.5980 chunk 151 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 46 optimal weight: 20.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4071 r_free = 0.4071 target = 0.148311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.093505 restraints weight = 18405.071| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.81 r_work: 0.3151 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13460 Z= 0.112 Angle : 0.462 9.246 18180 Z= 0.246 Chirality : 0.041 0.170 2036 Planarity : 0.003 0.042 2328 Dihedral : 3.643 20.205 1768 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.82 % Allowed : 16.98 % Favored : 82.20 % 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: 2.31 (0.21), residues: 1600 helix: 3.19 (0.18), residues: 686 sheet: 0.44 (0.38), residues: 212 loop : 0.23 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 27 HIS 0.002 0.001 HIS D 161 PHE 0.013 0.001 PHE C 111 TYR 0.015 0.001 TYR A 167 ARG 0.007 0.000 ARG A 87 Details of bonding type rmsd hydrogen bonds : bond 0.03249 ( 662) hydrogen bonds : angle 4.26804 ( 1893) covalent geometry : bond 0.00257 (13460) covalent geometry : angle 0.46175 (18180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9200.39 seconds wall clock time: 159 minutes 10.37 seconds (9550.37 seconds total)