Starting phenix.real_space_refine on Wed Aug 5 04:33:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kic_37257/08_2026/8kic_37257.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kic_37257/08_2026/8kic_37257.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8kic_37257/08_2026/8kic_37257.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kic_37257/08_2026/8kic_37257.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kic_37257/08_2026/8kic_37257.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kic_37257/08_2026/8kic_37257.map" } resolution = 2.5 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 5374 2.51 5 N 1515 2.21 5 O 1683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8589 Number of models: 1 Model: "" Number of chains: 9 Chain: "D" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 632 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 3, 'TRANS': 83} Chain breaks: 1 Chain: "E" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 656 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain: "F" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 667 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "C" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2178 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 12, 'TRANS': 287} Chain breaks: 1 Chain: "A" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2178 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 12, 'TRANS': 287} Chain breaks: 1 Chain: "B" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2178 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 12, 'TRANS': 287} Chain breaks: 1 Chain: "G" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 25 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'UNK:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 35 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 1.92, per 1000 atoms: 0.22 Number of scatterers: 8589 At special positions: 0 Unit cell: (89.04, 125.504, 122.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 17 16.00 O 1683 8.00 N 1515 7.00 C 5374 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: 0.63 Conformation dependent library (CDL) restraints added in 392.4 milliseconds 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2094 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 20 sheets defined 21.8% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'D' and resid 372 through 376 Processing helix chain 'D' and resid 401 through 407 Processing helix chain 'D' and resid 424 through 433 Processing helix chain 'E' and resid 372 through 376 Processing helix chain 'E' and resid 401 through 407 Processing helix chain 'E' and resid 424 through 433 Processing helix chain 'F' and resid 372 through 376 Processing helix chain 'F' and resid 401 through 407 Processing helix chain 'F' and resid 424 through 433 Processing helix chain 'C' and resid 42 through 50 removed outlier: 4.200A pdb=" N LYS C 48 " --> pdb=" O PRO C 44 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL C 49 " --> pdb=" O MET C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 162 removed outlier: 3.513A pdb=" N LEU C 162 " --> pdb=" O SER C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 removed outlier: 3.658A pdb=" N GLY C 176 " --> pdb=" O ASN C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 262 Processing helix chain 'C' and resid 277 through 285 Processing helix chain 'C' and resid 301 through 307 Processing helix chain 'C' and resid 324 through 335 removed outlier: 3.808A pdb=" N LEU C 328 " --> pdb=" O SER C 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 50 removed outlier: 4.467A pdb=" N LYS A 48 " --> pdb=" O PRO A 44 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 49 " --> pdb=" O MET A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 112 Processing helix chain 'A' and resid 158 through 162 removed outlier: 3.607A pdb=" N LEU A 162 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.592A pdb=" N GLY A 176 " --> pdb=" O ASN A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 301 through 307 Processing helix chain 'A' and resid 324 through 335 removed outlier: 3.611A pdb=" N LEU A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 50 removed outlier: 4.233A pdb=" N LYS B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 49 " --> pdb=" O MET B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 112 removed outlier: 3.835A pdb=" N ILE B 111 " --> pdb=" O ASN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 removed outlier: 3.541A pdb=" N LYS B 161 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 162 " --> pdb=" O SER B 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 158 through 162' Processing helix chain 'B' and resid 173 through 177 removed outlier: 3.731A pdb=" N GLY B 176 " --> pdb=" O ASN B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 Processing helix chain 'B' and resid 279 through 284 Processing helix chain 'B' and resid 301 through 307 Processing helix chain 'B' and resid 324 through 335 removed outlier: 3.741A pdb=" N LEU B 328 " --> pdb=" O SER B 324 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 366 through 367 Processing sheet with id=AA2, first strand: chain 'D' and resid 382 through 384 Processing sheet with id=AA3, first strand: chain 'E' and resid 366 through 367 removed outlier: 3.716A pdb=" N LEU E 380 " --> pdb=" O ALA E 366 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU E 396 " --> pdb=" O THR E 379 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 382 through 384 Processing sheet with id=AA5, first strand: chain 'E' and resid 439 through 440 removed outlier: 3.865A pdb=" N ILE E 439 " --> pdb=" O MET E 454 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 378 through 384 removed outlier: 6.387A pdb=" N THR F 379 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 53 through 60 removed outlier: 7.938A pdb=" N SER C 93 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ASN C 107 " --> pdb=" O SER C 93 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TYR C 103 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE C 140 " --> pdb=" O SER C 134 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER C 134 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU C 142 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE C 117 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N LEU C 131 " --> pdb=" O GLN C 115 " (cutoff:3.500A) removed outlier: 11.399A pdb=" N GLN C 115 " --> pdb=" O LEU C 131 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLU C 59 " --> pdb=" O GLN C 115 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE C 117 " --> pdb=" O ARG C 57 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ARG C 57 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE C 119 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER C 55 " --> pdb=" O ILE C 119 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 155 through 156 removed outlier: 7.263A pdb=" N ALA C 155 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N GLY C 227 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ASN C 229 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE C 246 " --> pdb=" O ASN C 229 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA C 231 " --> pdb=" O PHE C 244 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLN C 204 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N LEU C 189 " --> pdb=" O GLN C 204 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU C 218 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 271 through 275 removed outlier: 6.597A pdb=" N THR C 274 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL C 294 " --> pdb=" O THR C 274 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 271 through 275 removed outlier: 6.597A pdb=" N THR C 274 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL C 294 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY C 344 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU C 317 " --> pdb=" O LYS C 342 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LYS C 342 " --> pdb=" O LEU C 317 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 53 through 60 removed outlier: 7.809A pdb=" N SER A 93 " --> pdb=" O ASN A 107 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASN A 107 " --> pdb=" O SER A 93 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR A 103 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE A 140 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER A 134 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU A 142 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE A 117 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N LEU A 131 " --> pdb=" O GLN A 115 " (cutoff:3.500A) removed outlier: 11.749A pdb=" N GLN A 115 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLU A 59 " --> pdb=" O GLN A 115 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE A 117 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG A 57 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE A 119 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N SER A 55 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 30 through 31 removed outlier: 3.752A pdb=" N ILE A 232 " --> pdb=" O UNK G 30 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ASN A 229 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE A 246 " --> pdb=" O ASN A 229 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN A 204 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LEU A 189 " --> pdb=" O GLN A 204 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU A 218 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 267 through 268 removed outlier: 3.646A pdb=" N LEU A 268 " --> pdb=" O ASP A 359 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 271 through 275 removed outlier: 6.818A pdb=" N LYS A 272 " --> pdb=" O SER A 295 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 271 through 275 removed outlier: 6.818A pdb=" N LYS A 272 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLY A 344 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU A 317 " --> pdb=" O LYS A 342 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS A 342 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 53 through 60 removed outlier: 6.525A pdb=" N TYR B 103 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE B 140 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N SER B 134 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU B 142 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE B 117 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N LEU B 131 " --> pdb=" O GLN B 115 " (cutoff:3.500A) removed outlier: 11.671A pdb=" N GLN B 115 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 167 through 172 removed outlier: 5.345A pdb=" N PHE B 202 " --> pdb=" O GLY B 190 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N PHE B 244 " --> pdb=" O THR B 230 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU B 218 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 267 through 268 removed outlier: 3.588A pdb=" N ASP B 359 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 271 through 275 removed outlier: 6.693A pdb=" N THR B 274 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL B 294 " --> pdb=" O THR B 274 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 271 through 275 removed outlier: 6.693A pdb=" N THR B 274 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL B 294 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLY B 344 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU B 317 " --> pdb=" O LYS B 342 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LYS B 342 " --> pdb=" O LEU B 317 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 870 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: 1.48 Time building geometry restraints manager: 0.86 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: 1945 1.33 - 1.45: 1487 1.45 - 1.57: 5197 1.57 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 8663 Sorted by residual: bond pdb=" N ILE B 232 " pdb=" CA ILE B 232 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.08e-02 8.57e+03 1.52e+01 bond pdb=" N ILE D 443 " pdb=" CA ILE D 443 " ideal model delta sigma weight residual 1.459 1.507 -0.048 1.25e-02 6.40e+03 1.49e+01 bond pdb=" N ILE F 443 " pdb=" CA ILE F 443 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.25e-02 6.40e+03 1.43e+01 bond pdb=" N VAL F 444 " pdb=" CA VAL F 444 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.31e+00 bond pdb=" N ILE E 443 " pdb=" CA ILE E 443 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.25e+00 ... (remaining 8658 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 11574 3.14 - 6.28: 110 6.28 - 9.42: 8 9.42 - 12.56: 1 12.56 - 15.70: 3 Bond angle restraints: 11696 Sorted by residual: angle pdb=" C ILE D 438 " pdb=" N ILE D 439 " pdb=" CA ILE D 439 " ideal model delta sigma weight residual 122.93 115.75 7.18 1.31e+00 5.83e-01 3.00e+01 angle pdb=" N UNK G 29 " pdb=" CA UNK G 29 " pdb=" C UNK G 29 " ideal model delta sigma weight residual 110.74 95.04 15.70 3.00e+00 1.11e-01 2.74e+01 angle pdb=" N UNK G 30 " pdb=" CA UNK G 30 " pdb=" C UNK G 30 " ideal model delta sigma weight residual 110.74 97.52 13.22 3.00e+00 1.11e-01 1.94e+01 angle pdb=" CA LEU B 233 " pdb=" C LEU B 233 " pdb=" O LEU B 233 " ideal model delta sigma weight residual 120.70 115.99 4.71 1.08e+00 8.57e-01 1.90e+01 angle pdb=" N UNK G 33 " pdb=" CA UNK G 33 " pdb=" C UNK G 33 " ideal model delta sigma weight residual 110.74 123.52 -12.78 3.00e+00 1.11e-01 1.82e+01 ... (remaining 11691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 4579 17.54 - 35.07: 504 35.07 - 52.61: 161 52.61 - 70.14: 48 70.14 - 87.68: 15 Dihedral angle restraints: 5307 sinusoidal: 2032 harmonic: 3275 Sorted by residual: dihedral pdb=" CA UNK G 33 " pdb=" C UNK G 33 " pdb=" N UNK G 34 " pdb=" CA UNK G 34 " ideal model delta harmonic sigma weight residual -180.00 -155.02 -24.98 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CD ARG D 445 " pdb=" NE ARG D 445 " pdb=" CZ ARG D 445 " pdb=" NH1 ARG D 445 " ideal model delta sinusoidal sigma weight residual 0.00 36.07 -36.07 1 1.00e+01 1.00e-02 1.84e+01 dihedral pdb=" CA ASN A 201 " pdb=" C ASN A 201 " pdb=" N PHE A 202 " pdb=" CA PHE A 202 " ideal model delta harmonic sigma weight residual 180.00 -159.60 -20.40 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 5304 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1280 0.095 - 0.189: 127 0.189 - 0.284: 4 0.284 - 0.378: 2 0.378 - 0.473: 1 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CA UNK G 33 " pdb=" N UNK G 33 " pdb=" C UNK G 33 " pdb=" CB UNK G 33 " both_signs ideal model delta sigma weight residual False 2.52 2.05 0.47 2.00e-01 2.50e+01 5.58e+00 chirality pdb=" CB ILE B 111 " pdb=" CA ILE B 111 " pdb=" CG1 ILE B 111 " pdb=" CG2 ILE B 111 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CB VAL D 444 " pdb=" CA VAL D 444 " pdb=" CG1 VAL D 444 " pdb=" CG2 VAL D 444 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 1411 not shown) Planarity restraints: 1539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 445 " 0.638 9.50e-02 1.11e+02 2.86e-01 4.99e+01 pdb=" NE ARG D 445 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG D 445 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG D 445 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 445 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 336 " 0.065 5.00e-02 4.00e+02 9.75e-02 1.52e+01 pdb=" N PRO B 337 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO B 337 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 337 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 443 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.55e+00 pdb=" C ILE E 443 " 0.044 2.00e-02 2.50e+03 pdb=" O ILE E 443 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL E 444 " -0.015 2.00e-02 2.50e+03 ... (remaining 1536 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 334 2.72 - 3.26: 7630 3.26 - 3.81: 12822 3.81 - 4.35: 16367 4.35 - 4.90: 28390 Nonbonded interactions: 65543 Sorted by model distance: nonbonded pdb=" NZ LYS C 116 " pdb=" OD1 ASP C 128 " model vdw 2.171 3.120 nonbonded pdb=" OE2 GLU C 275 " pdb=" OG SER C 324 " model vdw 2.185 3.040 nonbonded pdb=" OG SER C 149 " pdb=" NZ LYS C 150 " model vdw 2.273 3.120 nonbonded pdb=" O GLY B 198 " pdb=" NH1 ARG B 329 " model vdw 2.298 3.120 nonbonded pdb=" OE1 GLU A 275 " pdb=" OG SER A 324 " model vdw 2.310 3.040 ... (remaining 65538 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = (chain 'E' and (resid 365 through 449 or resid 451 through 452)) selection = (chain 'F' and (resid 365 through 449 or resid 451 through 452)) } ncs_group { reference = (chain 'G' and resid 29 through 35) selection = chain 'I' } 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: 2.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.510 Find NCS groups from input model: 0.120 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: 0.000 Load rotamer database and sin/cos tables:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 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 : 0.005 0.074 8663 Z= 0.262 Angle : 0.816 15.696 11696 Z= 0.464 Chirality : 0.054 0.473 1414 Planarity : 0.010 0.286 1539 Dihedral : 17.673 87.678 3213 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.44 % Allowed : 2.26 % Favored : 97.30 % Rotamer: Outliers : 3.54 % Allowed : 23.56 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.24), residues: 1148 helix: 0.21 (0.38), residues: 195 sheet: 0.27 (0.28), residues: 324 loop : -0.44 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 419 TYR 0.008 0.002 TYR E 451 PHE 0.013 0.002 PHE C 127 HIS 0.005 0.002 HIS C 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.26 ( 8663) covalent geometry : angle 0.81555 / 0.46 (11696) hydrogen bonds : bond 0.17100 / 11.89 ( 321) hydrogen bonds : angle 7.10359 / 4.88 ( 870) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 15 residues processed: 128 average time/residue: 0.4529 time to fit residues: 62.2233 Evaluate side-chains 76 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 339 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.0470 chunk 100 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 55.6266 > 50:) overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 442 GLN A 107 ASN A 173 ASN ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.151036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.080641 restraints weight = 13139.076| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.21 r_work: 0.2819 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8663 Z= 0.124 Angle : 0.566 7.393 11696 Z= 0.291 Chirality : 0.046 0.214 1414 Planarity : 0.004 0.058 1539 Dihedral : 5.148 53.617 1246 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.44 % Favored : 97.30 % Rotamer: Outliers : 4.54 % Allowed : 22.68 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.25), residues: 1148 helix: 0.84 (0.40), residues: 195 sheet: 0.46 (0.29), residues: 313 loop : -0.27 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 419 TYR 0.005 0.001 TYR E 451 PHE 0.009 0.001 PHE C 127 HIS 0.003 0.002 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.12 ( 8663) covalent geometry : angle 0.56592 / 0.29 (11696) hydrogen bonds : bond 0.03083 / 2.07 ( 321) hydrogen bonds : angle 5.11279 / 3.47 ( 870) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 76 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: E 445 ARG cc_start: 0.5229 (ptp-110) cc_final: 0.4927 (tpm-80) REVERT: F 428 MET cc_start: 0.7166 (ttp) cc_final: 0.6610 (pp-130) REVERT: C 128 ASP cc_start: 0.8379 (m-30) cc_final: 0.7885 (t70) REVERT: A 282 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7751 (ttmt) REVERT: A 331 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7659 (mtt90) REVERT: B 139 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.8228 (t0) outliers start: 41 outliers final: 12 residues processed: 105 average time/residue: 0.3950 time to fit residues: 44.7572 Evaluate side-chains 79 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 294 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 91 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 12 optimal weight: 0.0970 chunk 2 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 19 optimal weight: 0.0770 chunk 26 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 ASN A 173 ASN ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.151345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.081411 restraints weight = 13142.576| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.21 r_work: 0.2854 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8663 Z= 0.095 Angle : 0.517 7.141 11696 Z= 0.264 Chirality : 0.045 0.197 1414 Planarity : 0.004 0.045 1539 Dihedral : 4.445 54.504 1232 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.18 % Favored : 97.56 % Rotamer: Outliers : 3.21 % Allowed : 24.45 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.25), residues: 1148 helix: 1.02 (0.39), residues: 195 sheet: 0.55 (0.29), residues: 313 loop : -0.04 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 331 TYR 0.002 0.000 TYR F 451 PHE 0.006 0.001 PHE C 127 HIS 0.002 0.001 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.09 ( 8663) covalent geometry : angle 0.51673 / 0.26 (11696) hydrogen bonds : bond 0.02609 / 1.73 ( 321) hydrogen bonds : angle 4.84328 / 3.27 ( 870) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 0.191 Fit side-chains REVERT: E 428 MET cc_start: 0.6768 (mmm) cc_final: 0.6046 (mtm) REVERT: F 428 MET cc_start: 0.7220 (ttp) cc_final: 0.6602 (pp-130) REVERT: C 128 ASP cc_start: 0.8399 (m-30) cc_final: 0.7890 (t70) REVERT: C 275 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8202 (mm-30) REVERT: A 173 ASN cc_start: 0.8627 (OUTLIER) cc_final: 0.8358 (t0) REVERT: A 331 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7733 (mtt90) outliers start: 29 outliers final: 12 residues processed: 85 average time/residue: 0.4407 time to fit residues: 40.2062 Evaluate side-chains 73 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 328 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.4980 chunk 53 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 213 ASN A 107 ASN A 173 ASN ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.148092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.078280 restraints weight = 13286.214| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.20 r_work: 0.2787 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8663 Z= 0.169 Angle : 0.573 8.130 11696 Z= 0.292 Chirality : 0.046 0.207 1414 Planarity : 0.004 0.039 1539 Dihedral : 4.718 57.254 1231 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.61 % Favored : 97.13 % Rotamer: Outliers : 3.32 % Allowed : 24.45 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.25), residues: 1148 helix: 1.23 (0.39), residues: 195 sheet: 0.42 (0.28), residues: 323 loop : -0.03 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 445 TYR 0.005 0.001 TYR F 451 PHE 0.012 0.001 PHE C 127 HIS 0.003 0.002 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.17 ( 8663) covalent geometry : angle 0.57253 / 0.29 (11696) hydrogen bonds : bond 0.03235 / 2.17 ( 321) hydrogen bonds : angle 4.98609 / 3.38 ( 870) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 61 time to evaluate : 0.326 Fit side-chains REVERT: E 370 MET cc_start: 0.6008 (pmm) cc_final: 0.5421 (pmm) REVERT: F 428 MET cc_start: 0.7228 (ttp) cc_final: 0.6563 (pp-130) REVERT: C 275 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.8044 (mm-30) REVERT: A 173 ASN cc_start: 0.8917 (OUTLIER) cc_final: 0.8611 (t0) REVERT: A 331 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7720 (mtt90) REVERT: B 139 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.7959 (t0) outliers start: 30 outliers final: 15 residues processed: 81 average time/residue: 0.4919 time to fit residues: 42.7628 Evaluate side-chains 76 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 328 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 74 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 0.0770 chunk 9 optimal weight: 9.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 ASN ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 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 = 0.4058 r_free = 0.4058 target = 0.148549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.077976 restraints weight = 13408.591| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.27 r_work: 0.2793 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8663 Z= 0.137 Angle : 0.542 9.014 11696 Z= 0.277 Chirality : 0.045 0.199 1414 Planarity : 0.003 0.035 1539 Dihedral : 4.587 59.264 1231 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.18 % Favored : 97.56 % Rotamer: Outliers : 3.65 % Allowed : 24.34 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.26), residues: 1148 helix: 1.30 (0.39), residues: 195 sheet: 0.37 (0.29), residues: 324 loop : -0.02 (0.26), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 445 TYR 0.006 0.001 TYR F 451 PHE 0.010 0.001 PHE C 127 HIS 0.002 0.001 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 8663) covalent geometry : angle 0.54196 / 0.28 (11696) hydrogen bonds : bond 0.02872 / 1.91 ( 321) hydrogen bonds : angle 4.89332 / 3.30 ( 870) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 59 time to evaluate : 0.287 Fit side-chains REVERT: D 421 ARG cc_start: 0.4852 (tpp80) cc_final: 0.4586 (tpp80) REVERT: E 370 MET cc_start: 0.5971 (pmm) cc_final: 0.5542 (pmm) REVERT: E 428 MET cc_start: 0.6083 (mmm) cc_final: 0.5321 (mtm) REVERT: F 428 MET cc_start: 0.7205 (ttp) cc_final: 0.6530 (pp-130) REVERT: C 275 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7997 (mm-30) REVERT: A 331 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7700 (mtt90) REVERT: B 139 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.7910 (t0) outliers start: 33 outliers final: 17 residues processed: 83 average time/residue: 0.4517 time to fit residues: 40.4858 Evaluate side-chains 76 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain E residue 450 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 339 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 76 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 17 optimal weight: 30.0000 chunk 45 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 92 optimal weight: 0.3980 chunk 100 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 ASN A 173 ASN ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.145628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.075731 restraints weight = 13255.178| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.22 r_work: 0.2756 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 8663 Z= 0.262 Angle : 0.625 9.519 11696 Z= 0.323 Chirality : 0.049 0.236 1414 Planarity : 0.004 0.039 1539 Dihedral : 5.025 57.314 1231 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.31 % Favored : 96.43 % Rotamer: Outliers : 3.98 % Allowed : 24.23 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.25), residues: 1148 helix: 1.24 (0.39), residues: 195 sheet: 0.21 (0.27), residues: 355 loop : -0.14 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 445 TYR 0.012 0.002 TYR D 451 PHE 0.017 0.001 PHE C 127 HIS 0.004 0.002 HIS C 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00653 / 0.26 ( 8663) covalent geometry : angle 0.62491 / 0.32 (11696) hydrogen bonds : bond 0.03887 / 2.61 ( 321) hydrogen bonds : angle 5.22160 / 3.54 ( 870) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 61 time to evaluate : 0.202 Fit side-chains REVERT: D 421 ARG cc_start: 0.5069 (tpp80) cc_final: 0.4852 (tpp80) REVERT: E 428 MET cc_start: 0.6361 (mmm) cc_final: 0.5729 (mtm) REVERT: F 428 MET cc_start: 0.7180 (ttp) cc_final: 0.6489 (pp-130) REVERT: A 173 ASN cc_start: 0.8937 (OUTLIER) cc_final: 0.8607 (t0) REVERT: B 139 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8097 (t0) outliers start: 36 outliers final: 17 residues processed: 87 average time/residue: 0.4376 time to fit residues: 41.0907 Evaluate side-chains 80 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 450 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 294 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 115 optimal weight: 6.9990 chunk 109 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 ASN ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 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 = 0.4052 r_free = 0.4052 target = 0.147827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.078166 restraints weight = 13327.095| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.24 r_work: 0.2791 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8663 Z= 0.126 Angle : 0.552 10.360 11696 Z= 0.279 Chirality : 0.045 0.195 1414 Planarity : 0.003 0.034 1539 Dihedral : 4.549 56.506 1231 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.18 % Favored : 97.56 % Rotamer: Outliers : 2.77 % Allowed : 25.55 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.26), residues: 1148 helix: 1.42 (0.40), residues: 195 sheet: 0.52 (0.29), residues: 312 loop : -0.11 (0.26), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 445 TYR 0.004 0.001 TYR F 451 PHE 0.009 0.001 PHE C 127 HIS 0.002 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 8663) covalent geometry : angle 0.55193 / 0.28 (11696) hydrogen bonds : bond 0.02735 / 1.80 ( 321) hydrogen bonds : angle 4.88769 / 3.28 ( 870) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: E 370 MET cc_start: 0.5387 (pmm) cc_final: 0.5039 (pmm) REVERT: E 393 LYS cc_start: 0.5925 (ptmm) cc_final: 0.5632 (pmmt) REVERT: E 428 MET cc_start: 0.6520 (mmm) cc_final: 0.5976 (mtm) REVERT: C 128 ASP cc_start: 0.8105 (p0) cc_final: 0.7611 (p0) REVERT: C 135 ASP cc_start: 0.7935 (t70) cc_final: 0.7328 (t0) REVERT: A 331 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7658 (mtt90) outliers start: 25 outliers final: 17 residues processed: 82 average time/residue: 0.4587 time to fit residues: 40.7455 Evaluate side-chains 79 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 450 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 339 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 99 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 105 optimal weight: 0.0470 chunk 80 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 ASN A 173 ASN ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.147487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.077167 restraints weight = 13256.242| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.25 r_work: 0.2778 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8663 Z= 0.157 Angle : 0.571 10.994 11696 Z= 0.288 Chirality : 0.046 0.192 1414 Planarity : 0.003 0.034 1539 Dihedral : 4.586 57.136 1231 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.87 % Favored : 96.86 % Rotamer: Outliers : 3.32 % Allowed : 25.11 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.26), residues: 1148 helix: 1.51 (0.39), residues: 195 sheet: 0.36 (0.29), residues: 327 loop : -0.09 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 445 TYR 0.006 0.001 TYR F 451 PHE 0.013 0.001 PHE C 127 HIS 0.002 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 ( 8663) covalent geometry : angle 0.57058 / 0.29 (11696) hydrogen bonds : bond 0.03091 / 2.05 ( 321) hydrogen bonds : angle 4.94583 / 3.34 ( 870) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 61 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 421 ARG cc_start: 0.4719 (tpp80) cc_final: 0.3934 (tpp-160) REVERT: F 454 MET cc_start: 0.5246 (pmm) cc_final: 0.4661 (pmm) REVERT: C 128 ASP cc_start: 0.8291 (p0) cc_final: 0.7805 (p0) REVERT: C 135 ASP cc_start: 0.7950 (t70) cc_final: 0.7348 (t0) REVERT: C 149 SER cc_start: 0.8437 (OUTLIER) cc_final: 0.8065 (p) REVERT: C 282 LYS cc_start: 0.9040 (mtpt) cc_final: 0.8802 (mttp) REVERT: A 331 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7708 (mtt90) REVERT: B 139 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8035 (t0) outliers start: 30 outliers final: 18 residues processed: 82 average time/residue: 0.4966 time to fit residues: 43.9638 Evaluate side-chains 81 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 450 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 339 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 6 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 ASN A 173 ASN ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.147029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.077099 restraints weight = 13186.793| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.23 r_work: 0.2776 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8663 Z= 0.174 Angle : 0.601 11.846 11696 Z= 0.299 Chirality : 0.047 0.186 1414 Planarity : 0.003 0.034 1539 Dihedral : 4.652 57.669 1231 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.61 % Favored : 97.13 % Rotamer: Outliers : 2.88 % Allowed : 25.55 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.26), residues: 1148 helix: 1.51 (0.39), residues: 195 sheet: 0.26 (0.28), residues: 337 loop : -0.03 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 445 TYR 0.006 0.001 TYR F 451 PHE 0.013 0.001 PHE C 127 HIS 0.003 0.002 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.17 ( 8663) covalent geometry : angle 0.60120 / 0.30 (11696) hydrogen bonds : bond 0.03139 / 2.08 ( 321) hydrogen bonds : angle 4.99974 / 3.38 ( 870) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 370 MET cc_start: 0.5175 (pmm) cc_final: 0.4929 (pmm) REVERT: E 393 LYS cc_start: 0.6469 (ptmm) cc_final: 0.6199 (pmmt) REVERT: E 428 MET cc_start: 0.5613 (mmm) cc_final: 0.4929 (mtm) REVERT: C 128 ASP cc_start: 0.8372 (p0) cc_final: 0.7913 (p0) REVERT: C 135 ASP cc_start: 0.7942 (t70) cc_final: 0.7326 (t0) REVERT: C 149 SER cc_start: 0.8434 (OUTLIER) cc_final: 0.8071 (p) REVERT: C 282 LYS cc_start: 0.9036 (mtpt) cc_final: 0.8788 (mttp) REVERT: A 331 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7709 (mtt90) REVERT: B 139 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8046 (t0) outliers start: 26 outliers final: 19 residues processed: 81 average time/residue: 0.4971 time to fit residues: 43.4181 Evaluate side-chains 82 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 450 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 339 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 54 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 85 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 103 optimal weight: 0.0070 chunk 18 optimal weight: 20.0000 chunk 57 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 ASN A 173 ASN ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.147968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.077995 restraints weight = 13249.933| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.24 r_work: 0.2795 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8663 Z= 0.134 Angle : 0.574 12.291 11696 Z= 0.284 Chirality : 0.046 0.210 1414 Planarity : 0.003 0.034 1539 Dihedral : 4.470 57.854 1231 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.35 % Favored : 97.39 % Rotamer: Outliers : 2.88 % Allowed : 25.66 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.26), residues: 1148 helix: 1.74 (0.39), residues: 192 sheet: 0.16 (0.28), residues: 349 loop : 0.11 (0.27), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 445 TYR 0.004 0.001 TYR D 451 PHE 0.010 0.001 PHE C 127 HIS 0.002 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.13 ( 8663) covalent geometry : angle 0.57389 / 0.28 (11696) hydrogen bonds : bond 0.02775 / 1.82 ( 321) hydrogen bonds : angle 4.85779 / 3.27 ( 870) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 421 ARG cc_start: 0.4714 (tpp80) cc_final: 0.4047 (tpp-160) REVERT: E 370 MET cc_start: 0.5091 (pmm) cc_final: 0.4828 (pmm) REVERT: E 393 LYS cc_start: 0.6476 (ptmm) cc_final: 0.6164 (pmmt) REVERT: E 428 MET cc_start: 0.5688 (mmm) cc_final: 0.4848 (mtm) REVERT: C 128 ASP cc_start: 0.8352 (p0) cc_final: 0.7894 (p0) REVERT: C 135 ASP cc_start: 0.7883 (t70) cc_final: 0.7319 (t0) REVERT: C 149 SER cc_start: 0.8422 (OUTLIER) cc_final: 0.8060 (p) REVERT: C 282 LYS cc_start: 0.9011 (mtpt) cc_final: 0.8797 (mttp) REVERT: A 331 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7686 (mtt90) outliers start: 26 outliers final: 20 residues processed: 80 average time/residue: 0.4928 time to fit residues: 42.6528 Evaluate side-chains 84 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 450 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 339 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 22 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 105 optimal weight: 0.0970 chunk 67 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 19 optimal weight: 0.0050 chunk 63 optimal weight: 1.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 ASN A 173 ASN ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.149339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.079807 restraints weight = 13318.623| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.25 r_work: 0.2835 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8663 Z= 0.096 Angle : 0.544 12.344 11696 Z= 0.270 Chirality : 0.045 0.212 1414 Planarity : 0.003 0.036 1539 Dihedral : 4.214 59.485 1231 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.92 % Favored : 97.82 % Rotamer: Outliers : 2.88 % Allowed : 25.55 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.26), residues: 1148 helix: 1.88 (0.39), residues: 192 sheet: 0.25 (0.29), residues: 349 loop : 0.23 (0.27), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 445 TYR 0.003 0.001 TYR B 103 PHE 0.006 0.001 PHE C 127 HIS 0.002 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 ( 8663) covalent geometry : angle 0.54408 / 0.27 (11696) hydrogen bonds : bond 0.02359 / 1.54 ( 321) hydrogen bonds : angle 4.68296 / 3.14 ( 870) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3571.76 seconds wall clock time: 61 minutes 19.43 seconds (3679.43 seconds total)