Starting phenix.real_space_refine on Thu Feb 13 02:23:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kic_37257/02_2025/8kic_37257.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kic_37257/02_2025/8kic_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8kic_37257/02_2025/8kic_37257.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kic_37257/02_2025/8kic_37257.map" model { file = "/net/cci-nas-00/data/ceres_data/8kic_37257/02_2025/8kic_37257.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kic_37257/02_2025/8kic_37257.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.010 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.78, per 1000 atoms: 0.67 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: 2.17 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.44 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: 2.70 Time building geometry restraints manager: 2.52 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: 2.990 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.010 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 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= 0.327 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (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 HIS 0.005 0.002 HIS C 109 PHE 0.013 0.002 PHE C 127 TYR 0.008 0.002 TYR E 451 ARG 0.012 0.001 ARG D 419 *********************** 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 : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 15 residues processed: 128 average time/residue: 1.0998 time to fit residues: 151.5056 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 : 0.979 ------------------------------------------------------------------------------- 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 97 optimal weight: 0.9980 chunk 87 optimal weight: 0.0970 chunk 48 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4077 r_free = 0.4077 target = 0.150838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.080490 restraints weight = 12981.655| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.18 r_work: 0.2816 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8663 Z= 0.209 Angle : 0.570 7.464 11696 Z= 0.293 Chirality : 0.046 0.213 1414 Planarity : 0.004 0.058 1539 Dihedral : 5.182 53.628 1246 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.61 % Favored : 97.13 % Rotamer: Outliers : 4.76 % Allowed : 22.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.25), residues: 1148 helix: 0.83 (0.40), residues: 195 sheet: 0.45 (0.29), residues: 313 loop : -0.28 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 109 PHE 0.010 0.001 PHE C 127 TYR 0.005 0.001 TYR E 451 ARG 0.007 0.000 ARG D 419 *********************** 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: 43 poor density : 74 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 445 ARG cc_start: 0.5317 (ptp-110) cc_final: 0.4993 (tpm-80) REVERT: F 428 MET cc_start: 0.7170 (ttp) cc_final: 0.6610 (pp-130) REVERT: C 128 ASP cc_start: 0.8391 (m-30) cc_final: 0.7901 (t70) REVERT: A 282 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7760 (ttmt) REVERT: A 331 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7692 (mtt90) REVERT: B 139 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8232 (t0) outliers start: 43 outliers final: 11 residues processed: 105 average time/residue: 1.0527 time to fit residues: 120.2325 Evaluate side-chains 77 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 443 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 27 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 86 optimal weight: 0.4980 chunk 87 optimal weight: 0.1980 chunk 46 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 103 optimal weight: 0.3980 chunk 55 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4080 r_free = 0.4080 target = 0.150657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.079988 restraints weight = 13304.932| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.25 r_work: 0.2824 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8663 Z= 0.174 Angle : 0.522 7.041 11696 Z= 0.267 Chirality : 0.045 0.206 1414 Planarity : 0.004 0.045 1539 Dihedral : 4.503 54.978 1232 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.09 % Favored : 97.65 % Rotamer: Outliers : 3.10 % Allowed : 24.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.25), residues: 1148 helix: 1.10 (0.39), residues: 195 sheet: 0.52 (0.29), residues: 313 loop : -0.08 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 109 PHE 0.008 0.001 PHE C 127 TYR 0.003 0.001 TYR F 451 ARG 0.007 0.001 ARG C 331 *********************** 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: 28 poor density : 70 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: F 428 MET cc_start: 0.7216 (ttp) cc_final: 0.6608 (pp-130) REVERT: C 128 ASP cc_start: 0.8425 (m-30) cc_final: 0.7910 (t70) REVERT: A 331 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7724 (mtt90) outliers start: 28 outliers final: 12 residues processed: 85 average time/residue: 1.1352 time to fit residues: 103.8492 Evaluate side-chains 72 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 294 VAL Chi-restraints excluded: chain A residue 271 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 91 LEU Chi-restraints excluded: chain B residue 294 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 94 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 33 optimal weight: 0.0060 chunk 50 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 95 optimal weight: 0.0570 chunk 89 optimal weight: 3.9990 chunk 87 optimal weight: 0.0980 overall best weight: 0.7916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4069 r_free = 0.4069 target = 0.149519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.078994 restraints weight = 13281.709| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.24 r_work: 0.2810 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8663 Z= 0.201 Angle : 0.541 8.106 11696 Z= 0.275 Chirality : 0.045 0.198 1414 Planarity : 0.003 0.039 1539 Dihedral : 4.508 57.395 1231 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.00 % Favored : 97.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.26), residues: 1148 helix: 1.30 (0.39), residues: 195 sheet: 0.49 (0.29), residues: 323 loop : 0.05 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 109 PHE 0.009 0.001 PHE C 127 TYR 0.003 0.001 TYR F 451 ARG 0.004 0.000 ARG E 445 *********************** 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 93 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 60 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: E 370 MET cc_start: 0.6028 (pmm) cc_final: 0.5426 (pmm) REVERT: F 428 MET cc_start: 0.7211 (ttp) cc_final: 0.6558 (pp-130) REVERT: C 128 ASP cc_start: 0.8447 (m-30) cc_final: 0.8243 (m-30) REVERT: A 331 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7741 (mtt90) REVERT: B 139 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8281 (t0) outliers start: 33 outliers final: 15 residues processed: 83 average time/residue: 1.1341 time to fit residues: 101.3716 Evaluate side-chains 74 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 20.0000 chunk 97 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 18 optimal weight: 30.0000 chunk 49 optimal weight: 0.0050 chunk 58 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 17 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 213 ASN A 107 ASN A 120 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.146985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.076414 restraints weight = 13260.814| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.25 r_work: 0.2775 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8663 Z= 0.344 Angle : 0.587 9.179 11696 Z= 0.302 Chirality : 0.047 0.217 1414 Planarity : 0.004 0.035 1539 Dihedral : 4.822 57.552 1231 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.79 % Favored : 96.95 % Rotamer: Outliers : 3.76 % Allowed : 24.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.26), residues: 1148 helix: 1.39 (0.39), residues: 195 sheet: 0.29 (0.27), residues: 353 loop : -0.03 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS C 109 PHE 0.015 0.001 PHE C 127 TYR 0.009 0.001 TYR F 451 ARG 0.007 0.000 ARG E 445 *********************** 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 93 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 59 time to evaluate : 0.965 Fit side-chains REVERT: E 370 MET cc_start: 0.6013 (pmm) cc_final: 0.5809 (pmm) REVERT: E 445 ARG cc_start: 0.4212 (ptm160) cc_final: 0.4010 (ptm160) REVERT: F 428 MET cc_start: 0.7168 (ttp) cc_final: 0.6488 (pp-130) REVERT: B 139 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8074 (t0) outliers start: 34 outliers final: 17 residues processed: 83 average time/residue: 1.0341 time to fit residues: 93.6013 Evaluate side-chains 73 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 294 VAL Chi-restraints excluded: chain A residue 111 ILE 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 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 339 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 13 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 17 optimal weight: 30.0000 chunk 54 optimal weight: 8.9990 chunk 98 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 73 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4059 r_free = 0.4059 target = 0.148424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.078735 restraints weight = 13113.699| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.21 r_work: 0.2802 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2790 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= 0.191 Angle : 0.523 9.811 11696 Z= 0.267 Chirality : 0.045 0.194 1414 Planarity : 0.003 0.033 1539 Dihedral : 4.457 58.170 1231 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.26 % Favored : 97.47 % Rotamer: Outliers : 3.87 % Allowed : 24.00 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.26), residues: 1148 helix: 1.46 (0.39), residues: 195 sheet: 0.46 (0.29), residues: 324 loop : 0.00 (0.26), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 109 PHE 0.008 0.001 PHE C 127 TYR 0.003 0.001 TYR F 451 ARG 0.004 0.000 ARG D 419 *********************** 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 98 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 63 time to evaluate : 0.804 Fit side-chains revert: symmetry clash REVERT: E 445 ARG cc_start: 0.4251 (ptm160) cc_final: 0.4044 (ptm160) REVERT: A 331 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7685 (mtt90) REVERT: B 139 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.7944 (t0) outliers start: 35 outliers final: 19 residues processed: 85 average time/residue: 1.0003 time to fit residues: 92.3701 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 : 1.053 ------------------------------------------------------------------------------- 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 415 ILE 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 294 VAL Chi-restraints excluded: chain A residue 91 LEU 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 328 LEU Chi-restraints excluded: chain B residue 339 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 91 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 17 optimal weight: 30.0000 chunk 21 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 57 optimal weight: 0.0030 chunk 111 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4074 r_free = 0.4074 target = 0.149073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.080656 restraints weight = 13220.909| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.08 r_work: 0.2886 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8663 Z= 0.188 Angle : 0.531 10.288 11696 Z= 0.268 Chirality : 0.045 0.185 1414 Planarity : 0.003 0.033 1539 Dihedral : 4.364 58.433 1231 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.18 % Favored : 97.56 % Rotamer: Outliers : 3.54 % Allowed : 24.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.26), residues: 1148 helix: 1.56 (0.39), residues: 195 sheet: 0.61 (0.29), residues: 319 loop : 0.10 (0.26), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 109 PHE 0.009 0.001 PHE C 127 TYR 0.003 0.001 TYR F 451 ARG 0.003 0.000 ARG D 445 *********************** 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 97 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 65 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: D 421 ARG cc_start: 0.4665 (tpp80) cc_final: 0.4047 (tpp-160) REVERT: E 370 MET cc_start: 0.5555 (pmm) cc_final: 0.5181 (pmm) REVERT: F 370 MET cc_start: 0.6837 (pp-130) cc_final: 0.6296 (pmm) REVERT: C 219 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8679 (mt) REVERT: A 331 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7826 (mtt90) REVERT: B 139 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8057 (t0) outliers start: 32 outliers final: 21 residues processed: 84 average time/residue: 0.9581 time to fit residues: 87.9783 Evaluate side-chains 86 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 415 ILE Chi-restraints excluded: chain E residue 450 ILE Chi-restraints excluded: chain E residue 452 LEU 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 91 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain A residue 91 LEU 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 328 LEU 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 61 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4067 r_free = 0.4067 target = 0.148423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.080137 restraints weight = 13223.562| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.06 r_work: 0.2875 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3022 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= 0.220 Angle : 0.562 11.003 11696 Z= 0.280 Chirality : 0.046 0.194 1414 Planarity : 0.003 0.038 1539 Dihedral : 4.420 56.710 1231 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.44 % Favored : 97.30 % Rotamer: Outliers : 3.65 % Allowed : 24.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.26), residues: 1148 helix: 1.60 (0.39), residues: 195 sheet: 0.44 (0.28), residues: 338 loop : 0.16 (0.27), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.002 HIS B 109 PHE 0.010 0.001 PHE C 127 TYR 0.004 0.001 TYR F 451 ARG 0.006 0.000 ARG E 445 *********************** 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 93 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 60 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: D 421 ARG cc_start: 0.4802 (tpp80) cc_final: 0.4010 (tpp-160) REVERT: E 370 MET cc_start: 0.5490 (pmm) cc_final: 0.5192 (pmm) REVERT: F 370 MET cc_start: 0.6849 (pp-130) cc_final: 0.6303 (pmm) REVERT: F 454 MET cc_start: 0.5244 (pmm) cc_final: 0.4682 (pmm) REVERT: C 149 SER cc_start: 0.8494 (OUTLIER) cc_final: 0.8146 (p) REVERT: C 219 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8700 (mt) REVERT: C 282 LYS cc_start: 0.9031 (mtpt) cc_final: 0.8781 (mttp) REVERT: A 331 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7826 (mtt90) REVERT: B 139 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8079 (t0) outliers start: 33 outliers final: 20 residues processed: 82 average time/residue: 1.0023 time to fit residues: 89.5040 Evaluate side-chains 84 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 441 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 149 SER Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 219 LEU 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 219 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 chunk 69 optimal weight: 0.0040 chunk 24 optimal weight: 20.0000 chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4069 r_free = 0.4069 target = 0.148551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.080474 restraints weight = 13232.275| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.06 r_work: 0.2879 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3171 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= 0.210 Angle : 0.565 11.901 11696 Z= 0.279 Chirality : 0.045 0.194 1414 Planarity : 0.003 0.033 1539 Dihedral : 4.377 57.669 1231 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.26 % Favored : 97.47 % Rotamer: Outliers : 3.32 % Allowed : 25.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.26), residues: 1148 helix: 1.70 (0.39), residues: 195 sheet: 0.46 (0.28), residues: 338 loop : 0.19 (0.27), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 109 PHE 0.009 0.001 PHE C 127 TYR 0.004 0.001 TYR F 451 ARG 0.009 0.000 ARG E 445 *********************** 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 92 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 62 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: D 421 ARG cc_start: 0.4874 (tpp80) cc_final: 0.4062 (tpp-160) REVERT: F 370 MET cc_start: 0.6805 (pp-130) cc_final: 0.6250 (pmm) REVERT: C 149 SER cc_start: 0.8511 (OUTLIER) cc_final: 0.8172 (p) REVERT: C 219 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8686 (mt) REVERT: C 282 LYS cc_start: 0.9007 (mtpt) cc_final: 0.8782 (mttp) REVERT: A 331 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7832 (mtt90) REVERT: B 139 ASP cc_start: 0.8591 (OUTLIER) cc_final: 0.8050 (t0) outliers start: 30 outliers final: 20 residues processed: 81 average time/residue: 1.0312 time to fit residues: 90.6874 Evaluate side-chains 86 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 441 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 149 SER Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 219 LEU 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 219 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 92 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 80 optimal weight: 0.0170 chunk 78 optimal weight: 0.0970 chunk 58 optimal weight: 0.7980 chunk 111 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 46 optimal weight: 0.4980 chunk 25 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4081 r_free = 0.4081 target = 0.149583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.081602 restraints weight = 13161.259| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.06 r_work: 0.2901 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8663 Z= 0.159 Angle : 0.562 12.394 11696 Z= 0.275 Chirality : 0.045 0.187 1414 Planarity : 0.003 0.035 1539 Dihedral : 4.217 58.276 1231 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.00 % Favored : 97.74 % Rotamer: Outliers : 3.32 % Allowed : 25.33 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.26), residues: 1148 helix: 1.66 (0.39), residues: 195 sheet: 0.51 (0.29), residues: 338 loop : 0.28 (0.27), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 109 PHE 0.006 0.001 PHE C 127 TYR 0.002 0.000 TYR B 103 ARG 0.009 0.000 ARG E 445 ********************** 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 94 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 64 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: D 421 ARG cc_start: 0.4882 (tpp80) cc_final: 0.4072 (tpp-160) REVERT: E 370 MET cc_start: 0.5475 (pmm) cc_final: 0.5138 (pmm) REVERT: E 428 MET cc_start: 0.5763 (mmm) cc_final: 0.5411 (mtt) REVERT: F 370 MET cc_start: 0.6768 (pp-130) cc_final: 0.6208 (pmm) REVERT: C 135 ASP cc_start: 0.7959 (t70) cc_final: 0.7421 (t0) REVERT: C 149 SER cc_start: 0.8493 (OUTLIER) cc_final: 0.8154 (p) REVERT: C 219 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8678 (mt) REVERT: C 282 LYS cc_start: 0.8993 (mtpt) cc_final: 0.8713 (mttp) REVERT: A 331 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7829 (mtt90) REVERT: B 219 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8747 (mt) outliers start: 30 outliers final: 17 residues processed: 82 average time/residue: 1.1169 time to fit residues: 99.5381 Evaluate side-chains 82 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 419 ARG Chi-restraints excluded: chain E residue 450 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 219 LEU 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 91 LEU Chi-restraints excluded: chain B residue 219 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 100 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 13 optimal weight: 0.0070 chunk 63 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 0.0670 chunk 42 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4066 r_free = 0.4066 target = 0.148946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.078932 restraints weight = 13408.044| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.27 r_work: 0.2812 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8663 Z= 0.200 Angle : 0.596 13.434 11696 Z= 0.293 Chirality : 0.046 0.188 1414 Planarity : 0.004 0.084 1539 Dihedral : 4.475 58.927 1231 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.26 % Favored : 97.47 % Rotamer: Outliers : 2.54 % Allowed : 26.33 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.26), residues: 1148 helix: 1.75 (0.39), residues: 195 sheet: 0.38 (0.28), residues: 349 loop : 0.32 (0.27), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 109 PHE 0.009 0.001 PHE C 127 TYR 0.004 0.001 TYR F 451 ARG 0.018 0.001 ARG E 419 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7313.72 seconds wall clock time: 129 minutes 13.91 seconds (7753.91 seconds total)