Starting phenix.real_space_refine on Fri Sep 11 08:30:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6avb_7008/09_2026/6avb_7008.cif Found real_map, /net/cci-nas-00/data/ceres_data/6avb_7008/09_2026/6avb_7008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6avb_7008/09_2026/6avb_7008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6avb_7008/09_2026/6avb_7008.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6avb_7008/09_2026/6avb_7008.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6avb_7008/09_2026/6avb_7008.cif" model { file = "/net/cci-nas-00/data/ceres_data/6avb_7008/09_2026/6avb_7008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6avb_7008/09_2026/6avb_7008.cif" } resolution = 3.9 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 0.007 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 60 5.16 5 C 5469 2.51 5 N 1458 2.21 5 O 1680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8673 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2864 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 19, 'TRANS': 347} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'SME:plan-1': 2, 'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: A, B Time building chain proxies: 1.97, per 1000 atoms: 0.23 Number of scatterers: 8673 At special positions: 0 Unit cell: (86.403, 89.526, 135.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 6 15.00 O 1680 8.00 N 1458 7.00 C 5469 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: 0.92 Conformation dependent library (CDL) restraints added in 301.7 milliseconds 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2034 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 15 sheets defined 41.7% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'C' and resid 55 through 61 removed outlier: 4.033A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 92 removed outlier: 3.670A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP C 86 " --> pdb=" O MET C 82 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR C 91 " --> pdb=" O HIS C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 123 removed outlier: 4.358A pdb=" N LYS C 118 " --> pdb=" O ALA C 114 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N THR C 120 " --> pdb=" O ARG C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 146 removed outlier: 4.066A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.551A pdb=" N TYR C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 205 through 216 removed outlier: 3.882A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 232 Processing helix chain 'C' and resid 257 through 263 Processing helix chain 'C' and resid 273 through 284 removed outlier: 3.672A pdb=" N THR C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 297 removed outlier: 4.249A pdb=" N LEU C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 320 removed outlier: 3.732A pdb=" N THR C 318 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 347 removed outlier: 4.070A pdb=" N GLY C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 356 removed outlier: 3.671A pdb=" N TRP C 356 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 365 removed outlier: 3.570A pdb=" N ALA C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 371 removed outlier: 4.008A pdb=" N ILE C 369 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N HIS C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 removed outlier: 4.033A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 92 removed outlier: 3.670A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TRP A 86 " --> pdb=" O MET A 82 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR A 91 " --> pdb=" O HIS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 123 removed outlier: 4.358A pdb=" N LYS A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N THR A 120 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 146 removed outlier: 4.066A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.552A pdb=" N TYR A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.882A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 232 Processing helix chain 'A' and resid 257 through 263 Processing helix chain 'A' and resid 273 through 284 removed outlier: 3.671A pdb=" N THR A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 284 " --> pdb=" O ASN A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 297 removed outlier: 4.249A pdb=" N LEU A 293 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 320 removed outlier: 3.732A pdb=" N THR A 318 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 347 removed outlier: 4.069A pdb=" N GLY A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 356 removed outlier: 3.672A pdb=" N TRP A 356 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 365 removed outlier: 3.570A pdb=" N ALA A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 removed outlier: 4.008A pdb=" N ILE A 369 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N HIS A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 removed outlier: 4.032A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 92 removed outlier: 3.670A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP B 86 " --> pdb=" O MET B 82 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR B 91 " --> pdb=" O HIS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 123 removed outlier: 4.358A pdb=" N LYS B 118 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N THR B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 146 removed outlier: 4.066A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.552A pdb=" N TYR B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 205 through 216 removed outlier: 3.882A pdb=" N ASP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 232 Processing helix chain 'B' and resid 257 through 263 Processing helix chain 'B' and resid 273 through 284 removed outlier: 3.672A pdb=" N THR B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 284 " --> pdb=" O ASN B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 297 removed outlier: 4.249A pdb=" N LEU B 293 " --> pdb=" O ILE B 289 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 320 removed outlier: 3.733A pdb=" N THR B 318 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 347 removed outlier: 4.070A pdb=" N GLY B 343 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 356 removed outlier: 3.672A pdb=" N TRP B 356 " --> pdb=" O GLN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 365 removed outlier: 3.570A pdb=" N ALA B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 removed outlier: 4.008A pdb=" N ILE B 369 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N HIS B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.749A pdb=" N LYS C 18 " --> pdb=" O ASP C 11 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C 104 " --> pdb=" O LEU C 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'C' and resid 150 through 151 Processing sheet with id=AA4, first strand: chain 'C' and resid 160 through 162 Processing sheet with id=AA5, first strand: chain 'C' and resid 240 through 242 removed outlier: 3.631A pdb=" N LEU C 242 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.748A pdb=" N LYS A 18 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 104 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'A' and resid 150 through 151 Processing sheet with id=AA9, first strand: chain 'A' and resid 160 through 162 Processing sheet with id=AB1, first strand: chain 'A' and resid 240 through 242 removed outlier: 3.630A pdb=" N LEU A 242 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.748A pdb=" N LYS B 18 " --> pdb=" O ASP B 11 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 104 " --> pdb=" O LEU B 8 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB4, first strand: chain 'B' and resid 150 through 151 Processing sheet with id=AB5, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AB6, first strand: chain 'B' and resid 240 through 242 removed outlier: 3.632A pdb=" N LEU B 242 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) 264 hydrogen bonds defined for protein. 657 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: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1452 1.30 - 1.42: 2208 1.42 - 1.55: 5086 1.55 - 1.68: 11 1.68 - 1.81: 108 Bond restraints: 8865 Sorted by residual: bond pdb=" CG HIC C 73 " pdb=" CD2 HIC C 73 " ideal model delta sigma weight residual 1.369 1.307 0.062 2.00e-02 2.50e+03 9.66e+00 bond pdb=" CG HIC A 73 " pdb=" CD2 HIC A 73 " ideal model delta sigma weight residual 1.369 1.307 0.062 2.00e-02 2.50e+03 9.64e+00 bond pdb=" CG HIC B 73 " pdb=" CD2 HIC B 73 " ideal model delta sigma weight residual 1.369 1.307 0.062 2.00e-02 2.50e+03 9.55e+00 bond pdb=" C HIC B 73 " pdb=" O HIC B 73 " ideal model delta sigma weight residual 1.231 1.169 0.062 2.00e-02 2.50e+03 9.54e+00 bond pdb=" C HIC C 73 " pdb=" O HIC C 73 " ideal model delta sigma weight residual 1.231 1.169 0.062 2.00e-02 2.50e+03 9.54e+00 ... (remaining 8860 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 11235 1.94 - 3.88: 607 3.88 - 5.82: 149 5.82 - 7.76: 39 7.76 - 9.70: 12 Bond angle restraints: 12042 Sorted by residual: angle pdb=" C CYS C 217 " pdb=" N TYR C 218 " pdb=" CA TYR C 218 " ideal model delta sigma weight residual 121.76 130.12 -8.36 2.19e+00 2.09e-01 1.46e+01 angle pdb=" C CYS A 217 " pdb=" N TYR A 218 " pdb=" CA TYR A 218 " ideal model delta sigma weight residual 121.76 130.11 -8.35 2.19e+00 2.09e-01 1.45e+01 angle pdb=" C CYS B 217 " pdb=" N TYR B 218 " pdb=" CA TYR B 218 " ideal model delta sigma weight residual 121.76 130.11 -8.35 2.19e+00 2.09e-01 1.45e+01 angle pdb=" N GLU A 224 " pdb=" CA GLU A 224 " pdb=" C GLU A 224 " ideal model delta sigma weight residual 110.80 103.60 7.20 2.13e+00 2.20e-01 1.14e+01 angle pdb=" N GLU C 224 " pdb=" CA GLU C 224 " pdb=" C GLU C 224 " ideal model delta sigma weight residual 110.80 103.65 7.15 2.13e+00 2.20e-01 1.13e+01 ... (remaining 12037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.21: 4929 16.21 - 32.42: 309 32.42 - 48.63: 60 48.63 - 64.84: 9 64.84 - 81.04: 9 Dihedral angle restraints: 5316 sinusoidal: 2136 harmonic: 3180 Sorted by residual: dihedral pdb=" CA ARG B 116 " pdb=" C ARG B 116 " pdb=" N GLU B 117 " pdb=" CA GLU B 117 " ideal model delta harmonic sigma weight residual 180.00 150.29 29.71 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA ARG C 116 " pdb=" C ARG C 116 " pdb=" N GLU C 117 " pdb=" CA GLU C 117 " ideal model delta harmonic sigma weight residual 180.00 150.33 29.67 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA ARG A 116 " pdb=" C ARG A 116 " pdb=" N GLU A 117 " pdb=" CA GLU A 117 " ideal model delta harmonic sigma weight residual 180.00 150.33 29.67 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 5313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 743 0.044 - 0.088: 406 0.088 - 0.132: 139 0.132 - 0.176: 44 0.176 - 0.220: 9 Chirality restraints: 1341 Sorted by residual: chirality pdb=" CA SME A 47 " pdb=" N SME A 47 " pdb=" C SME A 47 " pdb=" CB SME A 47 " both_signs ideal model delta sigma weight residual False 2.40 2.18 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA SME B 47 " pdb=" N SME B 47 " pdb=" C SME B 47 " pdb=" CB SME B 47 " both_signs ideal model delta sigma weight residual False 2.40 2.18 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA SME C 47 " pdb=" N SME C 47 " pdb=" C SME C 47 " pdb=" CB SME C 47 " both_signs ideal model delta sigma weight residual False 2.40 2.19 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1338 not shown) Planarity restraints: 1536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 101 " -0.041 5.00e-02 4.00e+02 6.11e-02 5.97e+00 pdb=" N PRO A 102 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 101 " -0.040 5.00e-02 4.00e+02 6.10e-02 5.94e+00 pdb=" N PRO B 102 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 102 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 102 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 101 " 0.040 5.00e-02 4.00e+02 6.09e-02 5.93e+00 pdb=" N PRO C 102 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 102 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 102 " 0.034 5.00e-02 4.00e+02 ... (remaining 1533 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 286 2.64 - 3.20: 9676 3.20 - 3.77: 13887 3.77 - 4.33: 19536 4.33 - 4.90: 29691 Nonbonded interactions: 73076 Sorted by model distance: nonbonded pdb=" OG1 THR B 358 " pdb=" OE1 GLU B 361 " model vdw 2.072 3.040 nonbonded pdb=" OG1 THR C 358 " pdb=" OE1 GLU C 361 " model vdw 2.072 3.040 nonbonded pdb=" OG1 THR A 358 " pdb=" OE1 GLU A 361 " model vdw 2.072 3.040 nonbonded pdb=" OG SER C 155 " pdb=" OG1 THR C 303 " model vdw 2.073 3.040 nonbonded pdb=" OG SER A 155 " pdb=" OG1 THR A 303 " model vdw 2.073 3.040 ... (remaining 73071 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'A' selection = chain 'B' } 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=0.00 max=1.00 mean=0.94 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.340 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.950 Find NCS groups from input model: 0.100 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:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 : 0.009 0.062 8865 Z= 0.406 Angle : 1.130 9.701 12042 Z= 0.573 Chirality : 0.061 0.220 1341 Planarity : 0.006 0.061 1536 Dihedral : 11.850 81.044 3282 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 27.42 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.92 % Favored : 86.80 % Rotamer: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Cbeta Deviations : 0.29 % 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: -5.00 (0.19), residues: 1068 helix: -4.19 (0.14), residues: 330 sheet: -1.74 (0.34), residues: 210 loop : -3.41 (0.20), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 254 TYR 0.028 0.003 TYR A 218 PHE 0.031 0.003 PHE B 262 TRP 0.018 0.003 TRP C 86 HIS 0.009 0.003 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00886 / 0.41 ( 8865) covalent geometry : angle 1.13049 / 0.57 (12042) hydrogen bonds : bond 0.28072 / 19.27 ( 264) hydrogen bonds : angle 11.17500 / 7.77 ( 657) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 118 LYS cc_start: 0.8422 (mtpp) cc_final: 0.7954 (tptp) REVERT: C 148 THR cc_start: 0.8234 (t) cc_final: 0.7978 (m) REVERT: C 153 LEU cc_start: 0.8606 (tt) cc_final: 0.8350 (tp) REVERT: C 159 VAL cc_start: 0.8680 (p) cc_final: 0.8405 (m) REVERT: C 325 MET cc_start: 0.8267 (ttp) cc_final: 0.8021 (mtt) REVERT: C 356 TRP cc_start: 0.7797 (m100) cc_final: 0.7327 (m100) REVERT: A 118 LYS cc_start: 0.8403 (mtpp) cc_final: 0.7902 (mtpt) REVERT: A 159 VAL cc_start: 0.8816 (p) cc_final: 0.8510 (m) REVERT: A 299 MET cc_start: 0.8180 (ptm) cc_final: 0.7877 (ppp) REVERT: A 315 LYS cc_start: 0.8382 (tttm) cc_final: 0.8171 (tppt) REVERT: A 356 TRP cc_start: 0.7818 (m100) cc_final: 0.7491 (m100) REVERT: B 79 TRP cc_start: 0.8017 (m100) cc_final: 0.6527 (m-90) REVERT: B 123 MET cc_start: 0.9097 (mmt) cc_final: 0.8869 (mmt) REVERT: B 159 VAL cc_start: 0.8789 (p) cc_final: 0.8456 (m) REVERT: B 299 MET cc_start: 0.8018 (ptm) cc_final: 0.7755 (ppp) REVERT: B 325 MET cc_start: 0.8278 (ttp) cc_final: 0.8072 (mtt) REVERT: B 354 GLN cc_start: 0.8559 (pm20) cc_final: 0.8074 (pm20) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.0965 time to fit residues: 32.7627 Evaluate side-chains 152 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 128 ASN C 280 ASN C 314 GLN A 128 ASN A 280 ASN A 314 GLN B 128 ASN B 280 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.091066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.081492 restraints weight = 24612.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.083485 restraints weight = 12310.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.084864 restraints weight = 7389.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.085771 restraints weight = 5015.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.086362 restraints weight = 3768.697| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8865 Z= 0.222 Angle : 0.956 9.148 12042 Z= 0.472 Chirality : 0.053 0.197 1341 Planarity : 0.006 0.056 1536 Dihedral : 9.386 59.416 1245 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer: Outliers : 4.45 % Allowed : 10.10 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -3.45 (0.22), residues: 1068 helix: -2.43 (0.25), residues: 315 sheet: -1.52 (0.34), residues: 210 loop : -2.50 (0.22), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 183 TYR 0.023 0.002 TYR B 218 PHE 0.019 0.003 PHE C 352 TRP 0.036 0.003 TRP A 79 HIS 0.009 0.002 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.22 ( 8865) covalent geometry : angle 0.95601 / 0.47 (12042) hydrogen bonds : bond 0.05036 / 3.37 ( 264) hydrogen bonds : angle 7.16212 / 5.00 ( 657) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 209 time to evaluate : 0.322 Fit side-chains REVERT: C 82 MET cc_start: 0.8525 (tpt) cc_final: 0.8215 (tpt) REVERT: C 159 VAL cc_start: 0.8689 (p) cc_final: 0.8379 (m) REVERT: C 216 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8557 (pp) REVERT: C 305 MET cc_start: 0.7719 (mpp) cc_final: 0.7406 (mpp) REVERT: C 356 TRP cc_start: 0.7719 (m100) cc_final: 0.7181 (m100) REVERT: A 148 THR cc_start: 0.8379 (t) cc_final: 0.8049 (m) REVERT: A 159 VAL cc_start: 0.8777 (p) cc_final: 0.8468 (m) REVERT: A 216 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8547 (pp) REVERT: A 299 MET cc_start: 0.7840 (ptm) cc_final: 0.7632 (ppp) REVERT: A 356 TRP cc_start: 0.7693 (m100) cc_final: 0.7315 (m100) REVERT: B 107 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8236 (tm-30) REVERT: B 137 GLN cc_start: 0.8598 (mm-40) cc_final: 0.8353 (mm110) REVERT: B 159 VAL cc_start: 0.8602 (p) cc_final: 0.8226 (m) REVERT: B 216 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8326 (pp) REVERT: B 355 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7147 (mpp) outliers start: 41 outliers final: 25 residues processed: 230 average time/residue: 0.0651 time to fit residues: 22.4381 Evaluate side-chains 184 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 355 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 6 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 67 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.092088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.082506 restraints weight = 24350.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.084538 restraints weight = 12248.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.085908 restraints weight = 7367.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.086829 restraints weight = 5008.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.087494 restraints weight = 3768.015| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8865 Z= 0.174 Angle : 0.874 11.970 12042 Z= 0.423 Chirality : 0.050 0.192 1341 Planarity : 0.005 0.052 1536 Dihedral : 8.326 58.056 1245 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer: Outliers : 4.89 % Allowed : 14.77 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.87 (0.23), residues: 1068 helix: -1.63 (0.26), residues: 339 sheet: -1.37 (0.35), residues: 210 loop : -2.28 (0.24), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 183 TYR 0.020 0.002 TYR B 218 PHE 0.013 0.002 PHE B 262 TRP 0.017 0.002 TRP B 79 HIS 0.003 0.001 HIS A 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 8865) covalent geometry : angle 0.87409 / 0.42 (12042) hydrogen bonds : bond 0.04252 / 2.86 ( 264) hydrogen bonds : angle 6.23705 / 4.42 ( 657) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: C 82 MET cc_start: 0.8537 (tpt) cc_final: 0.8086 (tpt) REVERT: C 159 VAL cc_start: 0.8605 (p) cc_final: 0.8311 (m) REVERT: C 216 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8444 (pp) REVERT: C 283 MET cc_start: 0.8448 (mmp) cc_final: 0.8084 (mmm) REVERT: C 349 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7872 (pp) REVERT: C 356 TRP cc_start: 0.7747 (m100) cc_final: 0.7256 (m100) REVERT: A 148 THR cc_start: 0.8430 (t) cc_final: 0.8106 (m) REVERT: A 159 VAL cc_start: 0.8753 (p) cc_final: 0.8485 (m) REVERT: A 216 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8541 (pp) REVERT: A 249 THR cc_start: 0.8596 (m) cc_final: 0.8395 (t) REVERT: A 283 MET cc_start: 0.8405 (mmp) cc_final: 0.8068 (mmm) REVERT: A 356 TRP cc_start: 0.7608 (m100) cc_final: 0.7147 (m100) REVERT: B 12 ASN cc_start: 0.7616 (m-40) cc_final: 0.7405 (m-40) REVERT: B 137 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8230 (mm-40) REVERT: B 159 VAL cc_start: 0.8571 (p) cc_final: 0.8217 (m) REVERT: B 315 LYS cc_start: 0.8339 (tppt) cc_final: 0.7637 (ttmm) REVERT: B 349 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8128 (pp) outliers start: 45 outliers final: 25 residues processed: 230 average time/residue: 0.0577 time to fit residues: 20.6961 Evaluate side-chains 186 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 12 ASN A 121 GLN B 40 HIS B 87 HIS B 128 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.089874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.080245 restraints weight = 24991.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.082235 restraints weight = 12570.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.083600 restraints weight = 7564.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.084523 restraints weight = 5162.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.085174 restraints weight = 3886.794| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8865 Z= 0.222 Angle : 0.902 7.771 12042 Z= 0.441 Chirality : 0.052 0.197 1341 Planarity : 0.005 0.053 1536 Dihedral : 8.567 59.519 1245 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.42 % Favored : 88.58 % Rotamer: Outliers : 6.30 % Allowed : 16.61 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.77 (0.23), residues: 1068 helix: -1.50 (0.26), residues: 339 sheet: -1.46 (0.34), residues: 210 loop : -2.18 (0.24), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 290 TYR 0.025 0.002 TYR C 166 PHE 0.014 0.002 PHE B 262 TRP 0.021 0.002 TRP B 79 HIS 0.004 0.002 HIS A 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.22 ( 8865) covalent geometry : angle 0.90188 / 0.44 (12042) hydrogen bonds : bond 0.04107 / 2.70 ( 264) hydrogen bonds : angle 6.04662 / 4.26 ( 657) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 170 time to evaluate : 0.333 Fit side-chains REVERT: C 133 TYR cc_start: 0.7735 (t80) cc_final: 0.7526 (t80) REVERT: C 159 VAL cc_start: 0.8696 (p) cc_final: 0.8391 (m) REVERT: C 349 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7884 (pp) REVERT: C 356 TRP cc_start: 0.7838 (m100) cc_final: 0.7538 (m100) REVERT: A 107 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8213 (tm-30) REVERT: A 137 GLN cc_start: 0.8272 (mm-40) cc_final: 0.7766 (mp10) REVERT: A 159 VAL cc_start: 0.8806 (p) cc_final: 0.8491 (m) REVERT: A 171 LEU cc_start: 0.9345 (mp) cc_final: 0.9066 (mp) REVERT: A 216 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8520 (pp) REVERT: A 221 LEU cc_start: 0.8028 (tp) cc_final: 0.7688 (tp) REVERT: A 283 MET cc_start: 0.8364 (mmp) cc_final: 0.8075 (mmm) REVERT: A 299 MET cc_start: 0.7816 (tmm) cc_final: 0.7358 (ppp) REVERT: A 356 TRP cc_start: 0.7645 (m100) cc_final: 0.7375 (m100) REVERT: B 137 GLN cc_start: 0.8405 (mm-40) cc_final: 0.8045 (mm-40) REVERT: B 159 VAL cc_start: 0.8606 (p) cc_final: 0.8258 (m) REVERT: B 315 LYS cc_start: 0.8409 (tppt) cc_final: 0.7671 (ttmm) outliers start: 58 outliers final: 34 residues processed: 207 average time/residue: 0.0621 time to fit residues: 19.6878 Evaluate side-chains 194 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 324 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 6 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 92 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.090017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.080453 restraints weight = 24674.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.082423 restraints weight = 12441.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.083815 restraints weight = 7521.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.084757 restraints weight = 5114.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.085423 restraints weight = 3827.293| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 8865 Z= 0.208 Angle : 0.897 8.699 12042 Z= 0.434 Chirality : 0.051 0.197 1341 Planarity : 0.005 0.052 1536 Dihedral : 8.440 59.498 1245 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.80 % Favored : 88.20 % Rotamer: Outliers : 5.21 % Allowed : 18.78 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.63 (0.24), residues: 1068 helix: -1.38 (0.26), residues: 345 sheet: -1.32 (0.35), residues: 210 loop : -2.15 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 290 TYR 0.025 0.002 TYR C 166 PHE 0.015 0.002 PHE A 127 TRP 0.021 0.002 TRP B 79 HIS 0.005 0.001 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 ( 8865) covalent geometry : angle 0.89659 / 0.43 (12042) hydrogen bonds : bond 0.03920 / 2.57 ( 264) hydrogen bonds : angle 6.02752 / 4.26 ( 657) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 169 time to evaluate : 0.333 Fit side-chains REVERT: C 82 MET cc_start: 0.8598 (tpt) cc_final: 0.8180 (tpt) REVERT: C 133 TYR cc_start: 0.7772 (t80) cc_final: 0.7418 (t80) REVERT: C 159 VAL cc_start: 0.8643 (p) cc_final: 0.8353 (m) REVERT: C 221 LEU cc_start: 0.8063 (tp) cc_final: 0.7775 (tp) REVERT: C 283 MET cc_start: 0.8428 (mmp) cc_final: 0.7934 (mmm) REVERT: C 349 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7892 (pp) REVERT: C 356 TRP cc_start: 0.7735 (m100) cc_final: 0.7457 (m100) REVERT: A 159 VAL cc_start: 0.8776 (p) cc_final: 0.8482 (m) REVERT: A 171 LEU cc_start: 0.9349 (mp) cc_final: 0.9122 (mp) REVERT: A 216 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8516 (pp) REVERT: A 283 MET cc_start: 0.8328 (mmp) cc_final: 0.8088 (mmm) REVERT: A 356 TRP cc_start: 0.7627 (m100) cc_final: 0.7237 (m100) REVERT: B 8 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7422 (pp) REVERT: B 137 GLN cc_start: 0.8343 (mm-40) cc_final: 0.7963 (mm-40) REVERT: B 159 VAL cc_start: 0.8581 (p) cc_final: 0.8247 (m) REVERT: B 315 LYS cc_start: 0.8460 (tppt) cc_final: 0.7663 (ttmm) REVERT: B 355 MET cc_start: 0.7675 (mtp) cc_final: 0.7463 (mpp) outliers start: 48 outliers final: 33 residues processed: 200 average time/residue: 0.0597 time to fit residues: 18.6132 Evaluate side-chains 190 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 324 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 84 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 53 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.090965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.081360 restraints weight = 24746.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.083371 restraints weight = 12437.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.084769 restraints weight = 7463.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.085636 restraints weight = 5078.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.086321 restraints weight = 3884.947| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8865 Z= 0.186 Angle : 0.892 11.328 12042 Z= 0.429 Chirality : 0.050 0.189 1341 Planarity : 0.005 0.050 1536 Dihedral : 8.253 58.285 1245 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.89 % Favored : 88.11 % Rotamer: Outliers : 4.99 % Allowed : 20.30 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.24), residues: 1068 helix: -1.19 (0.27), residues: 348 sheet: -1.32 (0.35), residues: 213 loop : -2.19 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 290 TYR 0.022 0.002 TYR B 218 PHE 0.013 0.002 PHE A 127 TRP 0.039 0.003 TRP A 79 HIS 0.005 0.001 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 ( 8865) covalent geometry : angle 0.89200 / 0.43 (12042) hydrogen bonds : bond 0.03704 / 2.42 ( 264) hydrogen bonds : angle 5.85315 / 4.15 ( 657) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 165 time to evaluate : 0.196 Fit side-chains REVERT: C 82 MET cc_start: 0.8581 (tpt) cc_final: 0.8163 (tpt) REVERT: C 159 VAL cc_start: 0.8596 (p) cc_final: 0.8336 (m) REVERT: C 221 LEU cc_start: 0.8106 (tp) cc_final: 0.7829 (tp) REVERT: C 283 MET cc_start: 0.8454 (mmp) cc_final: 0.7943 (mmm) REVERT: C 349 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7848 (pp) REVERT: C 356 TRP cc_start: 0.7651 (m100) cc_final: 0.7365 (m100) REVERT: A 159 VAL cc_start: 0.8729 (p) cc_final: 0.8463 (m) REVERT: A 171 LEU cc_start: 0.9346 (mp) cc_final: 0.9131 (mp) REVERT: A 216 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8488 (pp) REVERT: A 221 LEU cc_start: 0.7880 (tp) cc_final: 0.7560 (tp) REVERT: A 283 MET cc_start: 0.8352 (mmp) cc_final: 0.8085 (mmm) REVERT: A 299 MET cc_start: 0.7761 (tmm) cc_final: 0.7410 (ppp) REVERT: A 356 TRP cc_start: 0.7521 (m100) cc_final: 0.6970 (m100) REVERT: B 101 HIS cc_start: 0.5815 (OUTLIER) cc_final: 0.5421 (t-90) REVERT: B 159 VAL cc_start: 0.8567 (p) cc_final: 0.8248 (m) REVERT: B 315 LYS cc_start: 0.8403 (tppt) cc_final: 0.7570 (ttmm) REVERT: B 355 MET cc_start: 0.7716 (mtp) cc_final: 0.7486 (mpp) outliers start: 46 outliers final: 32 residues processed: 194 average time/residue: 0.0627 time to fit residues: 18.5268 Evaluate side-chains 183 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 324 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 12 optimal weight: 0.0050 chunk 55 optimal weight: 9.9990 chunk 87 optimal weight: 20.0000 chunk 101 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 40 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 overall best weight: 5.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 115 ASN A 314 GLN B 371 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.090365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.080734 restraints weight = 25072.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.082752 restraints weight = 12615.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.084137 restraints weight = 7598.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.085088 restraints weight = 5198.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.085656 restraints weight = 3912.291| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8865 Z= 0.201 Angle : 0.903 10.464 12042 Z= 0.434 Chirality : 0.050 0.193 1341 Planarity : 0.005 0.050 1536 Dihedral : 8.185 57.310 1245 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.11 % Favored : 86.89 % Rotamer: Outliers : 5.65 % Allowed : 20.96 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.67 (0.24), residues: 1068 helix: -1.33 (0.26), residues: 366 sheet: -1.25 (0.35), residues: 213 loop : -2.30 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 290 TYR 0.024 0.002 TYR B 218 PHE 0.015 0.002 PHE A 127 TRP 0.024 0.003 TRP B 79 HIS 0.005 0.001 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 ( 8865) covalent geometry : angle 0.90273 / 0.43 (12042) hydrogen bonds : bond 0.03634 / 2.43 ( 264) hydrogen bonds : angle 5.87530 / 4.15 ( 657) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 162 time to evaluate : 0.339 Fit side-chains REVERT: C 159 VAL cc_start: 0.8602 (p) cc_final: 0.8326 (m) REVERT: C 221 LEU cc_start: 0.8098 (tp) cc_final: 0.7848 (tp) REVERT: C 305 MET cc_start: 0.7949 (mpp) cc_final: 0.7697 (mpp) REVERT: C 349 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7971 (pp) REVERT: C 356 TRP cc_start: 0.7648 (m100) cc_final: 0.7418 (m100) REVERT: A 159 VAL cc_start: 0.8732 (p) cc_final: 0.8463 (m) REVERT: A 171 LEU cc_start: 0.9357 (mp) cc_final: 0.9115 (mp) REVERT: A 216 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8471 (pp) REVERT: A 283 MET cc_start: 0.8383 (mmp) cc_final: 0.8168 (mmm) REVERT: A 299 MET cc_start: 0.7694 (tmm) cc_final: 0.7283 (ppp) REVERT: A 313 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7964 (mtm) REVERT: A 356 TRP cc_start: 0.7632 (m100) cc_final: 0.7023 (m100) REVERT: B 101 HIS cc_start: 0.5471 (OUTLIER) cc_final: 0.5005 (t-90) REVERT: B 159 VAL cc_start: 0.8702 (p) cc_final: 0.8372 (m) REVERT: B 315 LYS cc_start: 0.8455 (tppt) cc_final: 0.7739 (ttmt) REVERT: B 354 GLN cc_start: 0.7871 (pm20) cc_final: 0.7465 (pm20) outliers start: 52 outliers final: 34 residues processed: 197 average time/residue: 0.0592 time to fit residues: 18.0107 Evaluate side-chains 187 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 324 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 58 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 13 optimal weight: 0.0670 chunk 41 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.091048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.081452 restraints weight = 24669.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.083426 restraints weight = 12490.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.084831 restraints weight = 7589.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.085791 restraints weight = 5181.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.086400 restraints weight = 3888.644| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8865 Z= 0.186 Angle : 0.886 11.030 12042 Z= 0.425 Chirality : 0.050 0.186 1341 Planarity : 0.005 0.049 1536 Dihedral : 8.106 58.003 1245 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.99 % Favored : 88.01 % Rotamer: Outliers : 4.89 % Allowed : 21.82 % Favored : 73.29 % 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: -2.67 (0.24), residues: 1068 helix: -1.32 (0.26), residues: 366 sheet: -1.14 (0.35), residues: 210 loop : -2.37 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 254 TYR 0.035 0.002 TYR A 166 PHE 0.013 0.002 PHE A 127 TRP 0.026 0.003 TRP B 79 HIS 0.006 0.001 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 ( 8865) covalent geometry : angle 0.88598 / 0.43 (12042) hydrogen bonds : bond 0.03573 / 2.39 ( 264) hydrogen bonds : angle 5.86902 / 4.15 ( 657) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 159 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: C 133 TYR cc_start: 0.7840 (t80) cc_final: 0.7363 (t80) REVERT: C 159 VAL cc_start: 0.8583 (p) cc_final: 0.8315 (m) REVERT: C 221 LEU cc_start: 0.8076 (tp) cc_final: 0.7829 (tp) REVERT: C 283 MET cc_start: 0.8523 (mmp) cc_final: 0.8061 (mmm) REVERT: C 305 MET cc_start: 0.7729 (mpp) cc_final: 0.7503 (mpp) REVERT: C 349 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7995 (pp) REVERT: C 356 TRP cc_start: 0.7531 (m100) cc_final: 0.7313 (m100) REVERT: A 159 VAL cc_start: 0.8725 (p) cc_final: 0.8460 (m) REVERT: A 171 LEU cc_start: 0.9370 (mp) cc_final: 0.9140 (mp) REVERT: A 216 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8466 (pp) REVERT: A 221 LEU cc_start: 0.7720 (tp) cc_final: 0.7501 (tp) REVERT: A 299 MET cc_start: 0.7648 (tmm) cc_final: 0.7205 (ppp) REVERT: A 356 TRP cc_start: 0.7578 (m100) cc_final: 0.7219 (m100) REVERT: B 101 HIS cc_start: 0.5568 (OUTLIER) cc_final: 0.5231 (t-90) REVERT: B 159 VAL cc_start: 0.8633 (p) cc_final: 0.8311 (m) REVERT: B 315 LYS cc_start: 0.8458 (tppt) cc_final: 0.7732 (ttmt) outliers start: 45 outliers final: 35 residues processed: 190 average time/residue: 0.0624 time to fit residues: 18.1900 Evaluate side-chains 190 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 324 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 64 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.092149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.082564 restraints weight = 24539.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.084634 restraints weight = 12414.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.085926 restraints weight = 7429.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.086925 restraints weight = 5146.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.087617 restraints weight = 3846.480| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8865 Z= 0.168 Angle : 0.893 11.468 12042 Z= 0.428 Chirality : 0.049 0.181 1341 Planarity : 0.005 0.049 1536 Dihedral : 7.938 58.548 1245 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.42 % Favored : 88.48 % Rotamer: Outliers : 4.45 % Allowed : 22.58 % Favored : 72.96 % 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: -2.36 (0.24), residues: 1068 helix: -1.07 (0.27), residues: 348 sheet: -0.98 (0.36), residues: 201 loop : -2.15 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 210 TYR 0.031 0.002 TYR A 166 PHE 0.016 0.002 PHE B 223 TRP 0.027 0.003 TRP B 79 HIS 0.010 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 ( 8865) covalent geometry : angle 0.89320 / 0.43 (12042) hydrogen bonds : bond 0.03396 / 2.25 ( 264) hydrogen bonds : angle 5.79093 / 4.12 ( 657) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 168 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 104 LEU cc_start: 0.8729 (tt) cc_final: 0.8428 (tp) REVERT: C 133 TYR cc_start: 0.7863 (t80) cc_final: 0.7603 (t80) REVERT: C 159 VAL cc_start: 0.8549 (p) cc_final: 0.8280 (m) REVERT: C 221 LEU cc_start: 0.8037 (tp) cc_final: 0.7804 (tp) REVERT: C 283 MET cc_start: 0.8511 (mmp) cc_final: 0.8091 (mmm) REVERT: C 349 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7975 (pp) REVERT: C 356 TRP cc_start: 0.7454 (m100) cc_final: 0.7218 (m100) REVERT: A 104 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8758 (tp) REVERT: A 159 VAL cc_start: 0.8781 (p) cc_final: 0.8498 (m) REVERT: A 171 LEU cc_start: 0.9318 (mp) cc_final: 0.9116 (mp) REVERT: A 216 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8493 (pp) REVERT: A 247 VAL cc_start: 0.8205 (OUTLIER) cc_final: 0.8005 (m) REVERT: A 356 TRP cc_start: 0.7505 (m100) cc_final: 0.7230 (m100) REVERT: B 101 HIS cc_start: 0.5181 (OUTLIER) cc_final: 0.4871 (t-90) REVERT: B 116 ARG cc_start: 0.6841 (ptt180) cc_final: 0.6495 (ptt90) REVERT: B 159 VAL cc_start: 0.8608 (p) cc_final: 0.8313 (m) REVERT: B 315 LYS cc_start: 0.8206 (tppt) cc_final: 0.7449 (ttmm) outliers start: 41 outliers final: 29 residues processed: 194 average time/residue: 0.0637 time to fit residues: 18.9290 Evaluate side-chains 190 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 324 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 45 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 35 optimal weight: 0.3980 chunk 50 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 38 optimal weight: 0.4980 chunk 101 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.092440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.082766 restraints weight = 24539.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.084800 restraints weight = 12453.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.086203 restraints weight = 7495.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.087164 restraints weight = 5096.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.087826 restraints weight = 3818.443| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.5679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8865 Z= 0.173 Angle : 0.924 13.435 12042 Z= 0.439 Chirality : 0.050 0.201 1341 Planarity : 0.005 0.053 1536 Dihedral : 7.897 59.304 1245 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.42 % Favored : 88.48 % Rotamer: Outliers : 4.02 % Allowed : 23.78 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.47 (0.24), residues: 1068 helix: -1.12 (0.27), residues: 348 sheet: -0.98 (0.36), residues: 204 loop : -2.28 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 290 TYR 0.033 0.002 TYR A 166 PHE 0.017 0.002 PHE B 223 TRP 0.030 0.003 TRP B 79 HIS 0.012 0.002 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 8865) covalent geometry : angle 0.92366 / 0.44 (12042) hydrogen bonds : bond 0.03404 / 2.26 ( 264) hydrogen bonds : angle 5.76843 / 4.11 ( 657) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 168 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: C 104 LEU cc_start: 0.8729 (tt) cc_final: 0.8395 (tp) REVERT: C 133 TYR cc_start: 0.7878 (t80) cc_final: 0.7609 (t80) REVERT: C 159 VAL cc_start: 0.8519 (p) cc_final: 0.8231 (m) REVERT: C 283 MET cc_start: 0.8513 (mmp) cc_final: 0.8099 (mmm) REVERT: C 355 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7298 (mpp) REVERT: C 356 TRP cc_start: 0.7449 (m100) cc_final: 0.7167 (m100) REVERT: A 159 VAL cc_start: 0.8779 (p) cc_final: 0.8499 (m) REVERT: A 216 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8507 (pp) REVERT: A 356 TRP cc_start: 0.7512 (m100) cc_final: 0.7203 (m100) REVERT: B 116 ARG cc_start: 0.6857 (ptt180) cc_final: 0.6494 (ptt90) REVERT: B 159 VAL cc_start: 0.8613 (p) cc_final: 0.8320 (m) REVERT: B 315 LYS cc_start: 0.8140 (tppt) cc_final: 0.7389 (ttmm) outliers start: 37 outliers final: 29 residues processed: 190 average time/residue: 0.0661 time to fit residues: 18.6678 Evaluate side-chains 192 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 324 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 75 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 83 optimal weight: 7.9990 chunk 67 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 371 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.091936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.082264 restraints weight = 24501.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.084328 restraints weight = 12444.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.085739 restraints weight = 7452.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.086683 restraints weight = 5072.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.087342 restraints weight = 3807.592| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.5715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8865 Z= 0.193 Angle : 0.932 14.054 12042 Z= 0.446 Chirality : 0.051 0.230 1341 Planarity : 0.006 0.053 1536 Dihedral : 7.879 54.324 1245 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.61 % Favored : 88.30 % Rotamer: Outliers : 3.69 % Allowed : 24.21 % Favored : 72.10 % 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: -2.52 (0.24), residues: 1068 helix: -1.15 (0.27), residues: 348 sheet: -1.06 (0.36), residues: 204 loop : -2.30 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 183 TYR 0.031 0.002 TYR A 166 PHE 0.016 0.002 PHE B 223 TRP 0.034 0.003 TRP B 79 HIS 0.013 0.002 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 ( 8865) covalent geometry : angle 0.93211 / 0.45 (12042) hydrogen bonds : bond 0.03493 / 2.33 ( 264) hydrogen bonds : angle 5.81847 / 4.14 ( 657) =============================================================================== Job complete usr+sys time: 1169.58 seconds wall clock time: 21 minutes 7.59 seconds (1267.59 seconds total)