Starting phenix.real_space_refine on Sun Jun 15 08:53:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ps4_17844/06_2025/8ps4_17844_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ps4_17844/06_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_17844/06_2025/8ps4_17844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ps4_17844/06_2025/8ps4_17844.map" model { file = "/net/cci-nas-00/data/ceres_data/8ps4_17844/06_2025/8ps4_17844_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ps4_17844/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.20, per 1000 atoms: 0.70 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: 3.35 Conformation dependent library (CDL) restraints added in 1.8 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: 1.64 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: 4.41 Time building geometry restraints manager: 3.96 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: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.680 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 34.280 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.470 ------------------------------------------------------------------------------- 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 : 1.690 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: 1.3189 time to fit residues: 342.2720 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 : 1.594 ------------------------------------------------------------------------------- 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 = 0.4093 r_free = 0.4093 target = 0.156456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.101088 restraints weight = 18800.273| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.68 r_work: 0.3306 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 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 17.569 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 5.12134 ( 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 : 1.631 Fit side-chains revert: symmetry clash REVERT: A 134 ILE cc_start: 0.7883 (OUTLIER) cc_final: 0.7481 (mm) REVERT: B 72 ASN cc_start: 0.7046 (m110) cc_final: 0.6707 (m-40) REVERT: B 100 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.6701 (tptm) REVERT: B 106 ARG cc_start: 0.8026 (mmm160) cc_final: 0.7645 (mmm160) REVERT: B 189 ARG cc_start: 0.8189 (mtp85) cc_final: 0.7933 (ttt90) REVERT: B 305 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.8173 (p) REVERT: C 1 MET cc_start: 0.6087 (pp-130) cc_final: 0.5762 (pp-130) REVERT: C 68 PHE cc_start: 0.7986 (t80) cc_final: 0.7270 (t80) REVERT: C 130 LYS cc_start: 0.7935 (mmmt) cc_final: 0.7476 (mptt) REVERT: C 216 ASP cc_start: 0.7756 (m-30) cc_final: 0.7346 (OUTLIER) REVERT: D 23 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7348 (tt) REVERT: D 79 PRO cc_start: 0.8374 (Cg_exo) cc_final: 0.8141 (Cg_endo) REVERT: D 177 ARG cc_start: 0.7744 (mmt90) cc_final: 0.7073 (mmm160) outliers start: 23 outliers final: 4 residues processed: 131 average time/residue: 1.1293 time to fit residues: 164.7948 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 : 1.690 ------------------------------------------------------------------------------- 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: 0.4980 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: 6.9990 chunk 138 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 65 optimal weight: 0.0370 overall best weight: 1.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 385 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.152229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.095403 restraints weight = 19064.530| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.71 r_work: 0.3209 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13460 Z= 0.141 Angle : 0.484 7.368 18180 Z= 0.265 Chirality : 0.043 0.177 2036 Planarity : 0.003 0.035 2328 Dihedral : 3.821 17.928 1768 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.49 % Allowed : 13.72 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.21), residues: 1600 helix: 3.29 (0.18), residues: 698 sheet: 0.93 (0.38), residues: 216 loop : 0.28 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 25 HIS 0.009 0.001 HIS B 321 PHE 0.015 0.001 PHE A 376 TYR 0.011 0.001 TYR B 256 ARG 0.005 0.000 ARG C 154 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 662) hydrogen bonds : angle 4.76953 ( 1893) covalent geometry : bond 0.00329 (13460) covalent geometry : angle 0.48380 (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 131 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 1.590 Fit side-chains revert: symmetry clash REVERT: A 134 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7790 (mt) REVERT: A 202 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7763 (mt) REVERT: B 72 ASN cc_start: 0.7257 (m110) cc_final: 0.6988 (m-40) REVERT: B 106 ARG cc_start: 0.8079 (mmm160) cc_final: 0.7667 (mmm160) REVERT: B 189 ARG cc_start: 0.8170 (mtp85) cc_final: 0.7897 (ttt90) REVERT: B 195 ASP cc_start: 0.7563 (t0) cc_final: 0.7343 (t0) REVERT: B 305 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8207 (p) REVERT: C 1 MET cc_start: 0.6120 (pp-130) cc_final: 0.5806 (pp-130) REVERT: C 68 PHE cc_start: 0.7934 (t80) cc_final: 0.7225 (t80) REVERT: C 130 LYS cc_start: 0.7958 (mmmt) cc_final: 0.7528 (mptt) REVERT: C 202 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7880 (mt) REVERT: C 216 ASP cc_start: 0.7743 (m-30) cc_final: 0.7366 (OUTLIER) REVERT: D 23 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7405 (tt) REVERT: D 79 PRO cc_start: 0.8569 (Cg_exo) cc_final: 0.8267 (Cg_endo) REVERT: D 177 ARG cc_start: 0.7813 (mmt90) cc_final: 0.7049 (mmm160) REVERT: D 226 GLU cc_start: 0.8038 (tt0) cc_final: 0.7772 (tt0) outliers start: 22 outliers final: 5 residues processed: 123 average time/residue: 1.1022 time to fit residues: 150.9482 Evaluate side-chains 99 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 173 ASP 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 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: 0.9980 chunk 2 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 124 optimal weight: 0.0470 chunk 115 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 362 GLN A 365 ASN B 362 GLN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.151272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.096501 restraints weight = 18802.905| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.86 r_work: 0.3102 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13460 Z= 0.197 Angle : 0.513 7.117 18180 Z= 0.279 Chirality : 0.044 0.185 2036 Planarity : 0.003 0.034 2328 Dihedral : 3.952 19.591 1768 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.83 % Allowed : 14.33 % 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: 2.28 (0.21), residues: 1600 helix: 3.09 (0.18), residues: 684 sheet: 0.54 (0.37), residues: 216 loop : 0.26 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 229 HIS 0.003 0.001 HIS D 92 PHE 0.014 0.001 PHE D 376 TYR 0.011 0.001 TYR A 392 ARG 0.005 0.000 ARG B 81 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 662) hydrogen bonds : angle 4.71786 ( 1893) covalent geometry : bond 0.00481 (13460) covalent geometry : angle 0.51336 (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: 27 poor density : 97 time to evaluate : 1.517 Fit side-chains revert: symmetry clash REVERT: A 136 LYS cc_start: 0.7884 (ttpp) cc_final: 0.7496 (tttp) REVERT: A 190 LYS cc_start: 0.9308 (tppt) cc_final: 0.9093 (mmmt) REVERT: A 202 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7816 (mt) REVERT: B 72 ASN cc_start: 0.7380 (m110) cc_final: 0.7126 (m-40) REVERT: B 305 THR cc_start: 0.8450 (OUTLIER) cc_final: 0.8142 (p) REVERT: C 1 MET cc_start: 0.6124 (pp-130) cc_final: 0.5779 (pp-130) REVERT: C 4 PHE cc_start: 0.7483 (m-80) cc_final: 0.7159 (m-80) REVERT: C 68 PHE cc_start: 0.7939 (t80) cc_final: 0.7277 (t80) REVERT: C 130 LYS cc_start: 0.8042 (mmmt) cc_final: 0.7625 (mptt) REVERT: C 202 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7837 (mt) REVERT: C 216 ASP cc_start: 0.7703 (m-30) cc_final: 0.7319 (OUTLIER) REVERT: C 286 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8172 (mmtp) REVERT: D 23 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7496 (tt) REVERT: D 79 PRO cc_start: 0.8553 (Cg_exo) cc_final: 0.8322 (Cg_endo) REVERT: D 100 LYS cc_start: 0.7729 (mtmm) cc_final: 0.7193 (ptmt) REVERT: D 177 ARG cc_start: 0.7846 (mmt90) cc_final: 0.7045 (mmm160) REVERT: D 193 LYS cc_start: 0.8555 (tppp) cc_final: 0.8200 (tptt) outliers start: 27 outliers final: 6 residues processed: 118 average time/residue: 1.0267 time to fit residues: 135.7642 Evaluate side-chains 97 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 1.694 ------------------------------------------------------------------------------- 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 305 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 153 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 78 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 120 optimal weight: 20.0000 chunk 37 optimal weight: 0.9980 chunk 12 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.149648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.092332 restraints weight = 18928.769| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.69 r_work: 0.3159 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13460 Z= 0.118 Angle : 0.458 8.505 18180 Z= 0.248 Chirality : 0.042 0.180 2036 Planarity : 0.003 0.033 2328 Dihedral : 3.771 19.226 1768 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.70 % Allowed : 15.08 % Favored : 83.22 % 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: 3.17 (0.18), residues: 686 sheet: 0.56 (0.37), residues: 216 loop : 0.23 (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 0.013 0.001 PHE A 376 TYR 0.011 0.001 TYR B 392 ARG 0.003 0.000 ARG C 154 Details of bonding type rmsd hydrogen bonds : bond 0.03462 ( 662) hydrogen bonds : angle 4.52330 ( 1893) covalent geometry : bond 0.00274 (13460) covalent geometry : angle 0.45823 (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 126 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 1.720 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3598 (tpp) cc_final: 0.3359 (tpp) REVERT: A 136 LYS cc_start: 0.7917 (ttpp) cc_final: 0.7566 (tttp) REVERT: A 202 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7894 (mt) REVERT: B 72 ASN cc_start: 0.7396 (m110) cc_final: 0.7149 (m-40) REVERT: B 190 LYS cc_start: 0.8440 (mtmm) cc_final: 0.8070 (mttm) REVERT: B 305 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8345 (p) REVERT: C 1 MET cc_start: 0.6052 (pp-130) cc_final: 0.5687 (pp-130) REVERT: C 4 PHE cc_start: 0.7429 (m-80) cc_final: 0.6950 (m-80) REVERT: C 68 PHE cc_start: 0.7907 (t80) cc_final: 0.7125 (t80) REVERT: C 117 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6843 (mp) REVERT: C 130 LYS cc_start: 0.7992 (mmmt) cc_final: 0.7623 (mptt) REVERT: C 202 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7977 (mt) REVERT: C 216 ASP cc_start: 0.7838 (m-30) cc_final: 0.7402 (OUTLIER) REVERT: D 79 PRO cc_start: 0.8499 (Cg_exo) cc_final: 0.8264 (Cg_endo) REVERT: D 100 LYS cc_start: 0.7717 (mtmm) cc_final: 0.7202 (ptmt) REVERT: D 177 ARG cc_start: 0.7940 (mmt90) cc_final: 0.7113 (mmm160) REVERT: D 193 LYS cc_start: 0.8531 (tppp) cc_final: 0.8165 (tptt) outliers start: 25 outliers final: 8 residues processed: 118 average time/residue: 1.0918 time to fit residues: 144.1147 Evaluate side-chains 98 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 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 84 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 202 LEU 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: 0.3980 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: 0.6980 chunk 24 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4010 r_free = 0.4010 target = 0.149409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.092001 restraints weight = 19019.916| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.69 r_work: 0.3154 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13460 Z= 0.123 Angle : 0.461 7.603 18180 Z= 0.249 Chirality : 0.042 0.179 2036 Planarity : 0.003 0.053 2328 Dihedral : 3.730 20.003 1768 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.43 % Allowed : 15.76 % Favored : 82.81 % 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: 2.29 (0.21), residues: 1600 helix: 3.18 (0.18), residues: 686 sheet: 0.55 (0.38), residues: 212 loop : 0.17 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 27 HIS 0.004 0.001 HIS A 120 PHE 0.012 0.001 PHE A 376 TYR 0.010 0.001 TYR D 392 ARG 0.012 0.000 ARG A 87 Details of bonding type rmsd hydrogen bonds : bond 0.03445 ( 662) hydrogen bonds : angle 4.44797 ( 1893) covalent geometry : bond 0.00286 (13460) covalent geometry : angle 0.46135 (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 111 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 1.491 Fit side-chains revert: symmetry clash REVERT: A 136 LYS cc_start: 0.7927 (ttpp) cc_final: 0.7573 (tttp) REVERT: A 202 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7826 (mt) REVERT: B 72 ASN cc_start: 0.7447 (m110) cc_final: 0.7221 (m-40) REVERT: B 305 THR cc_start: 0.8567 (OUTLIER) cc_final: 0.8332 (p) REVERT: C 1 MET cc_start: 0.6083 (pp-130) cc_final: 0.5694 (pp-130) REVERT: C 68 PHE cc_start: 0.7842 (t80) cc_final: 0.7055 (t80) REVERT: C 130 LYS cc_start: 0.8020 (mmmt) cc_final: 0.7553 (mptt) REVERT: C 202 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7965 (mt) REVERT: C 216 ASP cc_start: 0.7815 (m-30) cc_final: 0.7375 (t70) REVERT: D 79 PRO cc_start: 0.8507 (Cg_exo) cc_final: 0.8269 (Cg_endo) REVERT: D 106 ARG cc_start: 0.8441 (mmp-170) cc_final: 0.7941 (mmp80) REVERT: D 193 LYS cc_start: 0.8529 (tppp) cc_final: 0.8173 (tptt) outliers start: 21 outliers final: 8 residues processed: 105 average time/residue: 1.0620 time to fit residues: 124.9653 Evaluate side-chains 97 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 84 SER Chi-restraints excluded: chain C residue 202 LEU 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: 9.9990 chunk 3 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 63 optimal weight: 0.2980 chunk 144 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN B 92 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.150925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.093724 restraints weight = 18329.258| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.89 r_work: 0.3152 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13460 Z= 0.118 Angle : 0.455 7.616 18180 Z= 0.245 Chirality : 0.042 0.180 2036 Planarity : 0.003 0.044 2328 Dihedral : 3.671 19.901 1768 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.90 % Allowed : 15.56 % Favored : 82.54 % 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: 3.20 (0.18), residues: 686 sheet: 0.53 (0.38), residues: 212 loop : 0.17 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 27 HIS 0.003 0.001 HIS B 161 PHE 0.012 0.001 PHE A 376 TYR 0.012 0.001 TYR A 167 ARG 0.010 0.000 ARG A 87 Details of bonding type rmsd hydrogen bonds : bond 0.03360 ( 662) hydrogen bonds : angle 4.37943 ( 1893) covalent geometry : bond 0.00275 (13460) covalent geometry : angle 0.45462 (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 118 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 1.667 Fit side-chains revert: symmetry clash REVERT: A 136 LYS cc_start: 0.7991 (ttpp) cc_final: 0.7641 (tttp) REVERT: A 202 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7809 (mt) REVERT: B 72 ASN cc_start: 0.7541 (m110) cc_final: 0.7325 (m-40) REVERT: B 129 ASP cc_start: 0.8545 (p0) cc_final: 0.8054 (m-30) REVERT: B 305 THR cc_start: 0.8486 (OUTLIER) cc_final: 0.8270 (p) REVERT: C 1 MET cc_start: 0.6197 (pp-130) cc_final: 0.5726 (pp-130) REVERT: C 4 PHE cc_start: 0.7387 (m-80) cc_final: 0.6839 (m-80) REVERT: C 68 PHE cc_start: 0.7900 (t80) cc_final: 0.7062 (t80) REVERT: C 117 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6813 (mp) REVERT: C 130 LYS cc_start: 0.8082 (mmmt) cc_final: 0.7638 (mptt) REVERT: C 202 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7890 (mt) REVERT: C 216 ASP cc_start: 0.7703 (m-30) cc_final: 0.7348 (t70) REVERT: D 23 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.7642 (tt) REVERT: D 79 PRO cc_start: 0.8634 (Cg_exo) cc_final: 0.8406 (Cg_endo) REVERT: D 100 LYS cc_start: 0.7706 (mtmm) cc_final: 0.7160 (ptmt) REVERT: D 106 ARG cc_start: 0.8388 (mmp-170) cc_final: 0.7750 (mmp80) REVERT: D 193 LYS cc_start: 0.8524 (tppp) cc_final: 0.8203 (tptt) outliers start: 28 outliers final: 9 residues processed: 110 average time/residue: 0.9752 time to fit residues: 121.3490 Evaluate side-chains 100 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 1.632 ------------------------------------------------------------------------------- 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 C residue 82 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 234 ILE 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: 3.9990 chunk 110 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 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: 2.7990 ------------------------------------------------------------------------------- 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 ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.149186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.089957 restraints weight = 19006.804| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.74 r_work: 0.3084 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 13460 Z= 0.251 Angle : 0.548 10.317 18180 Z= 0.292 Chirality : 0.045 0.183 2036 Planarity : 0.004 0.042 2328 Dihedral : 3.950 20.424 1768 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.90 % Allowed : 15.62 % Favored : 82.47 % 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: 1.99 (0.21), residues: 1600 helix: 2.80 (0.18), residues: 686 sheet: 0.29 (0.37), residues: 212 loop : 0.20 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 27 HIS 0.003 0.001 HIS D 321 PHE 0.017 0.001 PHE A 111 TYR 0.012 0.002 TYR D 244 ARG 0.006 0.000 ARG A 87 Details of bonding type rmsd hydrogen bonds : bond 0.04287 ( 662) hydrogen bonds : angle 4.59257 ( 1893) covalent geometry : bond 0.00624 (13460) covalent geometry : angle 0.54765 (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: 28 poor density : 86 time to evaluate : 1.545 Fit side-chains revert: symmetry clash REVERT: A 136 LYS cc_start: 0.8001 (ttpp) cc_final: 0.7635 (tttp) REVERT: A 190 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8994 (mmmt) REVERT: A 202 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7920 (mt) REVERT: B 129 ASP cc_start: 0.8658 (p0) cc_final: 0.8148 (m-30) REVERT: B 305 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8265 (p) REVERT: C 1 MET cc_start: 0.6127 (pp-130) cc_final: 0.5691 (pp-130) REVERT: C 68 PHE cc_start: 0.7799 (t80) cc_final: 0.6643 (t80) REVERT: C 130 LYS cc_start: 0.8094 (mmmt) cc_final: 0.7631 (mptt) REVERT: C 202 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7941 (tt) REVERT: C 216 ASP cc_start: 0.7804 (m-30) cc_final: 0.7381 (OUTLIER) REVERT: D 23 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7545 (tt) REVERT: D 93 LYS cc_start: 0.8854 (pttp) cc_final: 0.8649 (pttp) REVERT: D 100 LYS cc_start: 0.7852 (mtmm) cc_final: 0.7292 (ptmt) REVERT: D 193 LYS cc_start: 0.8617 (tppp) cc_final: 0.8291 (tptt) outliers start: 28 outliers final: 8 residues processed: 107 average time/residue: 1.1279 time to fit residues: 134.3314 Evaluate side-chains 95 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 1.495 ------------------------------------------------------------------------------- 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 191 THR Chi-restraints excluded: chain A residue 202 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 C residue 82 ILE Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 153 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 156 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 152 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 HIS ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.149528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.093415 restraints weight = 18383.873| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.53 r_work: 0.3152 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13460 Z= 0.127 Angle : 0.475 8.788 18180 Z= 0.255 Chirality : 0.042 0.179 2036 Planarity : 0.003 0.041 2328 Dihedral : 3.835 20.870 1768 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.36 % Allowed : 16.51 % Favored : 82.13 % 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: 2.13 (0.21), residues: 1600 helix: 3.01 (0.18), residues: 686 sheet: 0.35 (0.37), residues: 212 loop : 0.17 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 27 HIS 0.003 0.001 HIS B 161 PHE 0.012 0.001 PHE C 4 TYR 0.013 0.001 TYR A 167 ARG 0.007 0.000 ARG A 87 Details of bonding type rmsd hydrogen bonds : bond 0.03536 ( 662) hydrogen bonds : angle 4.44655 ( 1893) covalent geometry : bond 0.00297 (13460) covalent geometry : angle 0.47510 (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 105 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 1.529 Fit side-chains revert: symmetry clash REVERT: A 136 LYS cc_start: 0.8040 (ttpp) cc_final: 0.7658 (tttp) REVERT: A 202 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7974 (mt) REVERT: B 129 ASP cc_start: 0.8607 (p0) cc_final: 0.8119 (m-30) REVERT: B 293 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7801 (mp) REVERT: B 305 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8359 (p) REVERT: B 313 MET cc_start: 0.8629 (tpp) cc_final: 0.8328 (mmm) REVERT: C 1 MET cc_start: 0.6067 (pp-130) cc_final: 0.5557 (pp-130) REVERT: C 4 PHE cc_start: 0.7550 (m-80) cc_final: 0.6941 (m-10) REVERT: C 68 PHE cc_start: 0.7838 (t80) cc_final: 0.6932 (t80) REVERT: C 130 LYS cc_start: 0.8101 (mmmt) cc_final: 0.7697 (mptt) REVERT: C 202 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8004 (mt) REVERT: C 216 ASP cc_start: 0.7857 (m-30) cc_final: 0.7441 (t70) REVERT: D 23 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7591 (tt) REVERT: D 93 LYS cc_start: 0.8872 (pttp) cc_final: 0.8657 (pttp) REVERT: D 100 LYS cc_start: 0.7790 (mtmm) cc_final: 0.7238 (ptmt) REVERT: D 193 LYS cc_start: 0.8585 (tppp) cc_final: 0.8271 (tptt) outliers start: 20 outliers final: 6 residues processed: 101 average time/residue: 1.2210 time to fit residues: 138.2932 Evaluate side-chains 94 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 1.949 ------------------------------------------------------------------------------- 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 171 MET 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: 1.9990 chunk 57 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 68 optimal weight: 0.0030 chunk 99 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- 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 = 0.152082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.093692 restraints weight = 18812.790| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.67 r_work: 0.3139 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13460 Z= 0.137 Angle : 0.483 9.160 18180 Z= 0.258 Chirality : 0.042 0.178 2036 Planarity : 0.003 0.042 2328 Dihedral : 3.783 20.559 1768 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.88 % Allowed : 16.98 % Favored : 82.13 % 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: 2.18 (0.21), residues: 1600 helix: 3.05 (0.18), residues: 686 sheet: 0.39 (0.37), residues: 212 loop : 0.19 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 27 HIS 0.003 0.001 HIS B 161 PHE 0.012 0.001 PHE C 4 TYR 0.010 0.001 TYR B 392 ARG 0.007 0.000 ARG A 87 Details of bonding type rmsd hydrogen bonds : bond 0.03519 ( 662) hydrogen bonds : angle 4.40931 ( 1893) covalent geometry : bond 0.00326 (13460) covalent geometry : angle 0.48282 (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 97 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 1.567 Fit side-chains revert: symmetry clash REVERT: A 136 LYS cc_start: 0.8086 (ttpp) cc_final: 0.7705 (tttp) REVERT: A 202 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7954 (mt) REVERT: B 68 PHE cc_start: 0.8553 (t80) cc_final: 0.8334 (t80) REVERT: B 129 ASP cc_start: 0.8605 (p0) cc_final: 0.8122 (m-30) REVERT: B 293 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7841 (mp) REVERT: B 305 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8399 (p) REVERT: B 313 MET cc_start: 0.8656 (tpp) cc_final: 0.8329 (mmm) REVERT: B 345 MET cc_start: 0.9209 (ttp) cc_final: 0.8980 (ttt) REVERT: C 130 LYS cc_start: 0.8117 (mmmt) cc_final: 0.7727 (mptt) REVERT: C 202 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8036 (mt) REVERT: C 216 ASP cc_start: 0.7876 (m-30) cc_final: 0.7466 (t70) REVERT: D 23 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7564 (tt) REVERT: D 100 LYS cc_start: 0.7871 (mtmm) cc_final: 0.7320 (ptmt) REVERT: D 193 LYS cc_start: 0.8588 (tppp) cc_final: 0.8271 (tptt) outliers start: 13 outliers final: 6 residues processed: 95 average time/residue: 1.0726 time to fit residues: 114.5485 Evaluate side-chains 94 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 1.683 ------------------------------------------------------------------------------- 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 171 MET 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: 2.9990 chunk 151 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 46 optimal weight: 20.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 HIS ** 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 = 0.4070 r_free = 0.4070 target = 0.148307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.093150 restraints weight = 18413.728| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.64 r_work: 0.3168 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13460 Z= 0.112 Angle : 0.467 9.142 18180 Z= 0.248 Chirality : 0.041 0.177 2036 Planarity : 0.003 0.042 2328 Dihedral : 3.673 20.307 1768 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.95 % Allowed : 17.05 % Favored : 82.00 % 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: 2.27 (0.21), residues: 1600 helix: 3.16 (0.18), residues: 686 sheet: 0.45 (0.38), 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 0.003 0.001 HIS B 161 PHE 0.011 0.001 PHE A 376 TYR 0.014 0.001 TYR A 167 ARG 0.007 0.000 ARG A 87 Details of bonding type rmsd hydrogen bonds : bond 0.03224 ( 662) hydrogen bonds : angle 4.31418 ( 1893) covalent geometry : bond 0.00257 (13460) covalent geometry : angle 0.46652 (18180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10012.42 seconds wall clock time: 172 minutes 32.54 seconds (10352.54 seconds total)