Starting phenix.real_space_refine on Sat Oct 11 19:26:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ps4_17844/10_2025/8ps4_17844_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ps4_17844/10_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_17844/10_2025/8ps4_17844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ps4_17844/10_2025/8ps4_17844.map" model { file = "/net/cci-nas-00/data/ceres_data/8ps4_17844/10_2025/8ps4_17844_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ps4_17844/10_2025/8ps4_17844_neut.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 3.73, per 1000 atoms: 0.28 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: 1.16 Conformation dependent library (CDL) restraints added in 643.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.41 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: 2.77 Time building geometry restraints manager: 1.57 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: 0.01 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: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.150 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 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:7.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.840 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG C 154 TYR 0.016 0.002 TYR B 392 PHE 0.013 0.002 PHE D 111 TRP 0.013 0.002 TRP A 325 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.01218 (13460) covalent geometry : angle 1.46367 (18180) hydrogen bonds : bond 0.16370 ( 662) hydrogen bonds : angle 6.81739 ( 1893) *********************** 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 : 0.521 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: 0.6757 time to fit residues: 174.0537 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 : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4096 r_free = 0.4096 target = 0.156691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.101212 restraints weight = 18965.668| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.70 r_work: 0.3303 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2098 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= 0.136 Angle : 0.509 6.215 18180 Z= 0.282 Chirality : 0.043 0.179 2036 Planarity : 0.003 0.032 2328 Dihedral : 3.885 17.799 1768 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 1.70 % Allowed : 12.57 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.79 (0.21), residues: 1600 helix: 3.56 (0.18), residues: 702 sheet: 1.10 (0.39), residues: 206 loop : 0.29 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 87 TYR 0.013 0.001 TYR A 167 PHE 0.018 0.001 PHE A 376 TRP 0.010 0.001 TRP D 25 HIS 0.004 0.001 HIS D 321 Details of bonding type rmsd covalent geometry : bond 0.00297 (13460) covalent geometry : angle 0.50914 (18180) hydrogen bonds : bond 0.04330 ( 662) hydrogen bonds : angle 5.07195 ( 1893) *********************** 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 139 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: B 72 ASN cc_start: 0.7069 (m110) cc_final: 0.6717 (m-40) REVERT: B 100 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.6700 (tptm) REVERT: B 106 ARG cc_start: 0.8025 (mmm160) cc_final: 0.7641 (mmm160) REVERT: B 189 ARG cc_start: 0.8176 (mtp85) cc_final: 0.7911 (ttt90) REVERT: B 305 THR cc_start: 0.8416 (OUTLIER) cc_final: 0.8168 (p) REVERT: C 68 PHE cc_start: 0.7963 (t80) cc_final: 0.7247 (t80) REVERT: C 130 LYS cc_start: 0.7925 (mmmt) cc_final: 0.7464 (mptt) REVERT: C 216 ASP cc_start: 0.7744 (m-30) cc_final: 0.7332 (OUTLIER) REVERT: D 23 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7329 (tt) REVERT: D 79 PRO cc_start: 0.8379 (Cg_exo) cc_final: 0.8143 (Cg_endo) REVERT: D 177 ARG cc_start: 0.7721 (mmt90) cc_final: 0.7031 (mmm160) outliers start: 25 outliers final: 4 residues processed: 134 average time/residue: 0.5739 time to fit residues: 84.5627 Evaluate side-chains 97 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 8 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 6 optimal weight: 30.0000 chunk 148 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 28 optimal weight: 0.0970 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.4115 r_free = 0.4115 target = 0.156108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.101718 restraints weight = 18766.383| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.58 r_work: 0.3252 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2584 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= 0.125 Angle : 0.474 7.391 18180 Z= 0.259 Chirality : 0.042 0.175 2036 Planarity : 0.003 0.036 2328 Dihedral : 3.759 17.574 1768 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.43 % Allowed : 13.72 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.66 (0.21), residues: 1600 helix: 3.39 (0.18), residues: 700 sheet: 1.01 (0.39), residues: 206 loop : 0.30 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 154 TYR 0.010 0.001 TYR B 392 PHE 0.015 0.001 PHE A 376 TRP 0.007 0.001 TRP D 25 HIS 0.008 0.001 HIS B 321 Details of bonding type rmsd covalent geometry : bond 0.00287 (13460) covalent geometry : angle 0.47376 (18180) hydrogen bonds : bond 0.03862 ( 662) hydrogen bonds : angle 4.73402 ( 1893) *********************** 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 130 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.583 Fit side-chains revert: symmetry clash REVERT: A 134 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7777 (mt) REVERT: A 202 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7869 (mt) REVERT: A 388 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7993 (t70) REVERT: B 72 ASN cc_start: 0.7205 (m110) cc_final: 0.6942 (m-40) REVERT: B 100 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.6833 (tptm) REVERT: B 106 ARG cc_start: 0.8120 (mmm160) cc_final: 0.7697 (mmm160) REVERT: B 189 ARG cc_start: 0.8196 (mtp85) cc_final: 0.7925 (ttt90) REVERT: B 195 ASP cc_start: 0.7563 (t0) cc_final: 0.7295 (t70) REVERT: C 1 MET cc_start: 0.5845 (pp-130) cc_final: 0.5561 (pp-130) REVERT: C 68 PHE cc_start: 0.7879 (t80) cc_final: 0.7047 (t80) REVERT: C 130 LYS cc_start: 0.7934 (mmmt) cc_final: 0.7493 (mptt) REVERT: C 216 ASP cc_start: 0.7883 (m-30) cc_final: 0.7438 (OUTLIER) REVERT: D 23 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7401 (tt) REVERT: D 79 PRO cc_start: 0.8564 (Cg_exo) cc_final: 0.8268 (Cg_endo) REVERT: D 177 ARG cc_start: 0.7865 (mmt90) cc_final: 0.7064 (mmm160) REVERT: D 226 GLU cc_start: 0.8145 (tt0) cc_final: 0.7891 (tt0) outliers start: 21 outliers final: 6 residues processed: 122 average time/residue: 0.5420 time to fit residues: 73.2694 Evaluate side-chains 100 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 173 ASP 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 72 ASN 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 45 optimal weight: 40.0000 chunk 76 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 20.0000 chunk 125 optimal weight: 0.0170 chunk 54 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 93 optimal weight: 0.0020 chunk 142 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 overall best weight: 1.1028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 362 GLN A 365 ASN B 31 ASN C 31 ASN D 161 HIS ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.151008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.093748 restraints weight = 18987.384| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.72 r_work: 0.3184 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3047 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= 0.132 Angle : 0.472 7.179 18180 Z= 0.256 Chirality : 0.042 0.187 2036 Planarity : 0.003 0.033 2328 Dihedral : 3.767 18.487 1768 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.90 % Allowed : 14.40 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.45 (0.21), residues: 1600 helix: 3.32 (0.18), residues: 686 sheet: 0.64 (0.38), residues: 212 loop : 0.23 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 154 TYR 0.011 0.001 TYR A 181 PHE 0.013 0.001 PHE A 376 TRP 0.010 0.001 TRP A 27 HIS 0.003 0.001 HIS B 321 Details of bonding type rmsd covalent geometry : bond 0.00310 (13460) covalent geometry : angle 0.47232 (18180) hydrogen bonds : bond 0.03621 ( 662) hydrogen bonds : angle 4.56350 ( 1893) *********************** 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 131 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 136 LYS cc_start: 0.7865 (ttpp) cc_final: 0.7479 (tttp) REVERT: A 190 LYS cc_start: 0.9316 (tppt) cc_final: 0.9110 (mmmt) REVERT: A 202 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7859 (mt) REVERT: B 72 ASN cc_start: 0.7347 (m110) cc_final: 0.7056 (m-40) REVERT: C 68 PHE cc_start: 0.7822 (t80) cc_final: 0.7314 (t80) REVERT: C 130 LYS cc_start: 0.8024 (mmmt) cc_final: 0.7554 (mptt) REVERT: C 202 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7929 (mt) REVERT: C 216 ASP cc_start: 0.7842 (m-30) cc_final: 0.7408 (OUTLIER) REVERT: D 79 PRO cc_start: 0.8592 (Cg_exo) cc_final: 0.8369 (Cg_endo) REVERT: D 177 ARG cc_start: 0.7891 (mmt90) cc_final: 0.7057 (mmm160) REVERT: D 193 LYS cc_start: 0.8539 (tppp) cc_final: 0.8195 (tptt) REVERT: D 226 GLU cc_start: 0.8231 (tt0) cc_final: 0.7999 (tt0) outliers start: 28 outliers final: 7 residues processed: 124 average time/residue: 0.5235 time to fit residues: 71.9781 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 : 0.624 ------------------------------------------------------------------------------- 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 C residue 82 ILE Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain D residue 255 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 18 optimal weight: 9.9990 chunk 152 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 47 optimal weight: 0.0570 chunk 107 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 118 optimal weight: 0.7980 overall best weight: 1.3300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 ASN B 72 ASN B 92 HIS B 362 GLN ** 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 = 0.4016 r_free = 0.4016 target = 0.149855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.092245 restraints weight = 19104.792| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.71 r_work: 0.3157 rms_B_bonded: 3.15 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: 0.8048 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13460 Z= 0.145 Angle : 0.477 7.453 18180 Z= 0.258 Chirality : 0.042 0.178 2036 Planarity : 0.003 0.056 2328 Dihedral : 3.776 19.616 1768 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.49 % Allowed : 15.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.21), residues: 1600 helix: 3.22 (0.18), residues: 686 sheet: 0.51 (0.37), residues: 216 loop : 0.22 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 81 TYR 0.010 0.001 TYR B 392 PHE 0.013 0.001 PHE A 376 TRP 0.012 0.001 TRP A 27 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00346 (13460) covalent geometry : angle 0.47679 (18180) hydrogen bonds : bond 0.03637 ( 662) hydrogen bonds : angle 4.52688 ( 1893) *********************** 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 124 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 LYS cc_start: 0.7902 (ttpp) cc_final: 0.7542 (tttp) REVERT: A 202 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7831 (mt) REVERT: B 72 ASN cc_start: 0.7370 (m-40) cc_final: 0.7125 (m-40) REVERT: B 190 LYS cc_start: 0.8438 (mtmm) cc_final: 0.8050 (mttm) REVERT: B 362 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7930 (pm20) REVERT: C 1 MET cc_start: 0.5847 (pp-130) cc_final: 0.5488 (pp-130) REVERT: C 4 PHE cc_start: 0.7206 (m-80) cc_final: 0.6901 (m-80) REVERT: C 68 PHE cc_start: 0.7730 (t80) cc_final: 0.7307 (t80) REVERT: C 130 LYS cc_start: 0.8019 (mmmt) cc_final: 0.7448 (mptt) REVERT: C 202 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7931 (mt) REVERT: C 216 ASP cc_start: 0.7829 (m-30) cc_final: 0.7390 (OUTLIER) REVERT: D 23 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7528 (tt) REVERT: D 79 PRO cc_start: 0.8553 (Cg_exo) cc_final: 0.8322 (Cg_endo) REVERT: D 100 LYS cc_start: 0.7674 (mtmm) cc_final: 0.7142 (ptmt) REVERT: D 106 ARG cc_start: 0.8459 (mmp-170) cc_final: 0.7846 (mmp80) REVERT: D 177 ARG cc_start: 0.7915 (mmt90) cc_final: 0.7080 (mmm160) REVERT: D 193 LYS cc_start: 0.8517 (tppp) cc_final: 0.8160 (tptt) outliers start: 22 outliers final: 9 residues processed: 119 average time/residue: 0.5352 time to fit residues: 70.6913 Evaluate side-chains 106 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 9 ASN Chi-restraints excluded: chain B residue 100 LYS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 126 optimal weight: 20.0000 chunk 116 optimal weight: 0.9990 chunk 85 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 87 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 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 = 0.4001 r_free = 0.4001 target = 0.148734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.090889 restraints weight = 18963.496| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.70 r_work: 0.3135 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13460 Z= 0.160 Angle : 0.485 7.754 18180 Z= 0.261 Chirality : 0.043 0.177 2036 Planarity : 0.003 0.043 2328 Dihedral : 3.796 19.909 1768 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.56 % Allowed : 16.10 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.23 (0.21), residues: 1600 helix: 3.13 (0.18), residues: 686 sheet: 0.49 (0.35), residues: 232 loop : 0.14 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 81 TYR 0.010 0.001 TYR B 392 PHE 0.013 0.001 PHE C 102 TRP 0.007 0.001 TRP C 229 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00388 (13460) covalent geometry : angle 0.48463 (18180) hydrogen bonds : bond 0.03693 ( 662) hydrogen bonds : angle 4.50842 ( 1893) *********************** 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 117 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 LYS cc_start: 0.7946 (ttpp) cc_final: 0.7589 (tttp) REVERT: A 202 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7849 (mt) REVERT: B 72 ASN cc_start: 0.7442 (m-40) cc_final: 0.7227 (m-40) REVERT: B 190 LYS cc_start: 0.8445 (mtmm) cc_final: 0.8098 (mttm) REVERT: B 362 GLN cc_start: 0.8218 (pp30) cc_final: 0.7271 (pp30) REVERT: C 68 PHE cc_start: 0.7723 (t80) cc_final: 0.7386 (t80) REVERT: C 79 PRO cc_start: 0.8521 (Cg_exo) cc_final: 0.8305 (Cg_endo) REVERT: C 130 LYS cc_start: 0.8060 (mmmt) cc_final: 0.7480 (mptt) REVERT: C 202 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7930 (mt) REVERT: C 216 ASP cc_start: 0.7813 (m-30) cc_final: 0.7368 (OUTLIER) REVERT: D 23 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7547 (tt) REVERT: D 79 PRO cc_start: 0.8571 (Cg_exo) cc_final: 0.8344 (Cg_endo) REVERT: D 100 LYS cc_start: 0.7744 (mtmm) cc_final: 0.7218 (ptmt) REVERT: D 106 ARG cc_start: 0.8439 (mmp-170) cc_final: 0.7801 (mmp80) REVERT: D 193 LYS cc_start: 0.8531 (tppp) cc_final: 0.8187 (tptt) outliers start: 23 outliers final: 10 residues processed: 111 average time/residue: 0.5662 time to fit residues: 69.6749 Evaluate side-chains 101 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER 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 292 ILE 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 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 1 optimal weight: 40.0000 chunk 153 optimal weight: 0.0470 chunk 89 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 41 optimal weight: 30.0000 chunk 108 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 overall best weight: 1.0482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN B 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.150622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.093421 restraints weight = 18445.566| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.88 r_work: 0.3151 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3547 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= 0.125 Angle : 0.462 7.887 18180 Z= 0.249 Chirality : 0.041 0.173 2036 Planarity : 0.003 0.051 2328 Dihedral : 3.713 19.986 1768 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.49 % Allowed : 15.90 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.29 (0.21), residues: 1600 helix: 3.19 (0.18), residues: 686 sheet: 0.50 (0.38), residues: 212 loop : 0.18 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 81 TYR 0.011 0.001 TYR D 392 PHE 0.013 0.001 PHE A 376 TRP 0.006 0.001 TRP D 325 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00294 (13460) covalent geometry : angle 0.46179 (18180) hydrogen bonds : bond 0.03417 ( 662) hydrogen bonds : angle 4.41490 ( 1893) *********************** 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 112 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 LYS cc_start: 0.7985 (ttpp) cc_final: 0.7627 (tttp) REVERT: A 202 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7803 (mt) REVERT: B 129 ASP cc_start: 0.8517 (p0) cc_final: 0.7997 (m-30) REVERT: C 68 PHE cc_start: 0.7827 (t80) cc_final: 0.7510 (t80) REVERT: C 130 LYS cc_start: 0.8111 (mmmt) cc_final: 0.7622 (mptt) REVERT: C 202 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7871 (mt) REVERT: C 216 ASP cc_start: 0.7722 (m-30) cc_final: 0.7349 (t70) REVERT: D 23 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.7617 (tt) REVERT: D 79 PRO cc_start: 0.8635 (Cg_exo) cc_final: 0.8401 (Cg_endo) REVERT: D 100 LYS cc_start: 0.7742 (mtmm) cc_final: 0.7209 (ptmt) REVERT: D 106 ARG cc_start: 0.8362 (mmp-170) cc_final: 0.7690 (mmp80) REVERT: D 193 LYS cc_start: 0.8508 (tppp) cc_final: 0.8208 (tptt) outliers start: 22 outliers final: 9 residues processed: 106 average time/residue: 0.5032 time to fit residues: 59.5573 Evaluate side-chains 98 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 292 ILE 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 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 96 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 43 optimal weight: 0.1980 chunk 49 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 ASN B 92 HIS ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 GLN C 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.150118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.091327 restraints weight = 18766.382| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.71 r_work: 0.3109 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 0.050 13460 Z= 0.205 Angle : 0.521 9.013 18180 Z= 0.280 Chirality : 0.044 0.182 2036 Planarity : 0.004 0.042 2328 Dihedral : 3.904 20.491 1768 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.97 % Allowed : 15.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.08 (0.21), residues: 1600 helix: 2.94 (0.18), residues: 686 sheet: 0.32 (0.37), residues: 212 loop : 0.19 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 81 TYR 0.011 0.001 TYR D 244 PHE 0.015 0.001 PHE C 376 TRP 0.010 0.001 TRP C 229 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00509 (13460) covalent geometry : angle 0.52134 (18180) hydrogen bonds : bond 0.04051 ( 662) hydrogen bonds : angle 4.53526 ( 1893) *********************** 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 117 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 LYS cc_start: 0.7991 (ttpp) cc_final: 0.7617 (tttp) REVERT: A 190 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8978 (mmmt) REVERT: A 202 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7915 (mt) REVERT: B 129 ASP cc_start: 0.8617 (p0) cc_final: 0.8067 (m-30) REVERT: C 1 MET cc_start: 0.5927 (pp-130) cc_final: 0.5529 (pp-130) REVERT: C 4 PHE cc_start: 0.7301 (m-80) cc_final: 0.6690 (m-80) REVERT: C 68 PHE cc_start: 0.7861 (t80) cc_final: 0.7422 (t80) REVERT: C 130 LYS cc_start: 0.8072 (mmmt) cc_final: 0.7586 (mptt) REVERT: C 202 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7955 (mt) REVERT: C 216 ASP cc_start: 0.7810 (m-30) cc_final: 0.7382 (t70) REVERT: C 294 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7708 (mtt-85) REVERT: D 23 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7542 (tt) REVERT: D 79 PRO cc_start: 0.8613 (Cg_exo) cc_final: 0.8379 (Cg_endo) REVERT: D 93 LYS cc_start: 0.8846 (pttp) cc_final: 0.8625 (pttp) REVERT: D 100 LYS cc_start: 0.7862 (mtmm) cc_final: 0.7317 (ptmt) REVERT: D 106 ARG cc_start: 0.8409 (mmp-170) cc_final: 0.7730 (mmp80) REVERT: D 193 LYS cc_start: 0.8581 (tppp) cc_final: 0.8254 (tptt) outliers start: 29 outliers final: 7 residues processed: 108 average time/residue: 0.5393 time to fit residues: 64.4826 Evaluate side-chains 97 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 B residue 1 MET Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 100 LYS 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 294 ARG 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 87 optimal weight: 10.0000 chunk 121 optimal weight: 40.0000 chunk 75 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 chunk 114 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.4069 r_free = 0.4069 target = 0.149288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.091589 restraints weight = 18478.142| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.71 r_work: 0.3145 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3814 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= 0.126 Angle : 0.474 8.808 18180 Z= 0.255 Chirality : 0.042 0.177 2036 Planarity : 0.003 0.039 2328 Dihedral : 3.789 20.663 1768 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.09 % Allowed : 16.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.21), residues: 1600 helix: 3.08 (0.18), residues: 686 sheet: 0.38 (0.37), residues: 212 loop : 0.19 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 81 TYR 0.014 0.001 TYR A 167 PHE 0.012 0.001 PHE A 376 TRP 0.006 0.001 TRP D 325 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00297 (13460) covalent geometry : angle 0.47414 (18180) hydrogen bonds : bond 0.03480 ( 662) hydrogen bonds : angle 4.40870 ( 1893) *********************** 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 101 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 LYS cc_start: 0.7986 (ttpp) cc_final: 0.7628 (tttp) REVERT: A 202 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7892 (mt) REVERT: B 129 ASP cc_start: 0.8609 (p0) cc_final: 0.8070 (m-30) REVERT: C 1 MET cc_start: 0.5942 (pp-130) cc_final: 0.5504 (pp-130) REVERT: C 4 PHE cc_start: 0.7233 (m-80) cc_final: 0.6729 (m-80) REVERT: C 68 PHE cc_start: 0.7789 (t80) cc_final: 0.7264 (t80) REVERT: C 130 LYS cc_start: 0.8100 (mmmt) cc_final: 0.7681 (mptt) REVERT: C 202 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7932 (mt) REVERT: C 216 ASP cc_start: 0.7809 (m-30) cc_final: 0.7363 (t70) REVERT: D 23 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7578 (tt) REVERT: D 93 LYS cc_start: 0.8836 (pttp) cc_final: 0.8617 (pttp) REVERT: D 100 LYS cc_start: 0.7756 (mtmm) cc_final: 0.7222 (ptmt) REVERT: D 106 ARG cc_start: 0.8415 (mmp-170) cc_final: 0.7652 (mmp80) REVERT: D 193 LYS cc_start: 0.8568 (tppp) cc_final: 0.8241 (tptt) outliers start: 16 outliers final: 6 residues processed: 99 average time/residue: 0.5353 time to fit residues: 58.9956 Evaluate side-chains 93 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 1 MET Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 100 LYS 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 86 optimal weight: 30.0000 chunk 102 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 124 optimal weight: 0.0870 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 ASN ** 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 = 0.4068 r_free = 0.4068 target = 0.152006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.093895 restraints weight = 18841.367| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.69 r_work: 0.3148 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13460 Z= 0.132 Angle : 0.474 9.166 18180 Z= 0.254 Chirality : 0.042 0.176 2036 Planarity : 0.003 0.038 2328 Dihedral : 3.736 20.282 1768 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.95 % Allowed : 16.98 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.21), residues: 1600 helix: 3.12 (0.18), residues: 686 sheet: 0.42 (0.38), residues: 212 loop : 0.22 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 81 TYR 0.010 0.001 TYR B 392 PHE 0.012 0.001 PHE A 376 TRP 0.006 0.001 TRP D 325 HIS 0.002 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00312 (13460) covalent geometry : angle 0.47384 (18180) hydrogen bonds : bond 0.03452 ( 662) hydrogen bonds : angle 4.34773 ( 1893) ********************** 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 : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 LYS cc_start: 0.8077 (ttpp) cc_final: 0.7701 (tttp) REVERT: A 202 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7937 (mt) REVERT: B 68 PHE cc_start: 0.8581 (t80) cc_final: 0.7997 (t80) REVERT: B 129 ASP cc_start: 0.8570 (p0) cc_final: 0.8048 (m-30) REVERT: B 313 MET cc_start: 0.8654 (tpp) cc_final: 0.8263 (mmm) REVERT: C 1 MET cc_start: 0.5996 (pp-130) cc_final: 0.5504 (pp-130) REVERT: C 4 PHE cc_start: 0.7229 (m-80) cc_final: 0.6729 (m-80) REVERT: C 68 PHE cc_start: 0.7829 (t80) cc_final: 0.7253 (t80) REVERT: C 130 LYS cc_start: 0.8116 (mmmt) cc_final: 0.7714 (mptt) REVERT: C 136 LYS cc_start: 0.7627 (mppt) cc_final: 0.7421 (mmpt) REVERT: C 202 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8014 (mt) REVERT: C 216 ASP cc_start: 0.7899 (m-30) cc_final: 0.7494 (t70) REVERT: D 23 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.7564 (tt) REVERT: D 100 LYS cc_start: 0.7883 (mtmm) cc_final: 0.7336 (ptmt) REVERT: D 106 ARG cc_start: 0.8437 (mmp-170) cc_final: 0.7678 (mmp80) REVERT: D 193 LYS cc_start: 0.8578 (tppp) cc_final: 0.8264 (tptt) outliers start: 14 outliers final: 8 residues processed: 100 average time/residue: 0.5438 time to fit residues: 60.4140 Evaluate side-chains 96 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 1 MET Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 100 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 67 optimal weight: 0.0670 chunk 87 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 138 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 overall best weight: 0.4920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.147518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.091045 restraints weight = 18354.430| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.71 r_work: 0.3184 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13460 Z= 0.099 Angle : 0.454 9.201 18180 Z= 0.243 Chirality : 0.041 0.172 2036 Planarity : 0.003 0.037 2328 Dihedral : 3.626 19.808 1768 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.02 % Allowed : 17.05 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.21), residues: 1600 helix: 3.26 (0.19), residues: 686 sheet: 0.50 (0.38), residues: 212 loop : 0.20 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 81 TYR 0.013 0.001 TYR A 167 PHE 0.011 0.001 PHE A 376 TRP 0.006 0.001 TRP B 325 HIS 0.003 0.000 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00217 (13460) covalent geometry : angle 0.45401 (18180) hydrogen bonds : bond 0.03069 ( 662) hydrogen bonds : angle 4.23964 ( 1893) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4946.91 seconds wall clock time: 84 minutes 57.15 seconds (5097.15 seconds total)