Starting phenix.real_space_refine on Fri Sep 11 08:41:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6av9_7007/09_2026/6av9_7007.cif Found real_map, /net/cci-nas-00/data/ceres_data/6av9_7007/09_2026/6av9_7007.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/6av9_7007/09_2026/6av9_7007.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6av9_7007/09_2026/6av9_7007.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6av9_7007/09_2026/6av9_7007.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6av9_7007/09_2026/6av9_7007.cif" model { file = "/net/cci-nas-00/data/ceres_data/6av9_7007/09_2026/6av9_7007.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6av9_7007/09_2026/6av9_7007.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 Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s 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: 2.36, per 1000 atoms: 0.27 Number of scatterers: 8673 At special positions: 0 Unit cell: (79.116, 93.69, 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: 0.88 Conformation dependent library (CDL) restraints added in 303.8 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: 48 helices and 12 sheets defined 40.1% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'C' and resid 55 through 61 removed outlier: 4.182A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.640A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR C 91 " --> pdb=" O HIS C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 122 removed outlier: 4.048A pdb=" N LYS C 118 " --> pdb=" O ALA C 114 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N THR C 120 " --> pdb=" O ARG C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 146 removed outlier: 3.809A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.771A pdb=" N THR C 186 " --> pdb=" O GLY C 182 " (cutoff:3.500A) removed outlier: 4.191A 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: 3.555A pdb=" N ILE C 212 " --> pdb=" O ILE C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 removed outlier: 3.726A pdb=" N MET C 227 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 260 removed outlier: 3.665A pdb=" N THR C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 283 removed outlier: 3.700A pdb=" N THR C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 297 removed outlier: 4.214A pdb=" N LEU C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 320 Processing helix chain 'C' and resid 337 through 347 removed outlier: 3.917A pdb=" N GLY C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 365 Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.736A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 removed outlier: 4.183A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.640A pdb=" N MET A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR A 91 " --> pdb=" O HIS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 122 removed outlier: 4.048A pdb=" N LYS A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N THR A 120 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 146 removed outlier: 3.809A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.771A pdb=" N THR A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) removed outlier: 4.192A 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: 3.556A pdb=" N ILE A 212 " --> pdb=" O ILE A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 removed outlier: 3.725A pdb=" N MET A 227 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 260 removed outlier: 3.665A pdb=" N THR A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 283 removed outlier: 3.700A pdb=" N THR A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 297 removed outlier: 4.214A pdb=" N LEU A 293 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 320 Processing helix chain 'A' and resid 337 through 347 removed outlier: 3.916A pdb=" N GLY A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 365 Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.736A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 removed outlier: 4.182A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.640A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B 91 " --> pdb=" O HIS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 122 removed outlier: 4.048A pdb=" N LYS B 118 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N THR B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 146 removed outlier: 3.810A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.771A pdb=" N THR B 186 " --> pdb=" O GLY B 182 " (cutoff:3.500A) removed outlier: 4.191A 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: 3.555A pdb=" N ILE B 212 " --> pdb=" O ILE B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 removed outlier: 3.726A pdb=" N MET B 227 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 260 removed outlier: 3.666A pdb=" N THR B 260 " --> pdb=" O ARG B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 283 removed outlier: 3.700A pdb=" N THR B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 297 removed outlier: 4.214A pdb=" N LEU B 293 " --> pdb=" O ILE B 289 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 320 Processing helix chain 'B' and resid 337 through 347 removed outlier: 3.917A pdb=" N GLY B 343 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 365 Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.735A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.653A 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: 3.650A 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 160 through 162 removed outlier: 3.591A pdb=" N THR C 160 " --> pdb=" O LEU C 178 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 165 through 166 Processing sheet with id=AA5, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.649A pdb=" N LEU A 104 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA7, first strand: chain 'A' and resid 160 through 162 removed outlier: 3.591A pdb=" N THR A 160 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 165 through 166 Processing sheet with id=AA9, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.650A pdb=" N LEU B 104 " --> pdb=" O LEU B 8 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'B' and resid 160 through 162 removed outlier: 3.591A pdb=" N THR B 160 " --> pdb=" O LEU B 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 165 through 166 252 hydrogen bonds defined for protein. 684 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: 1.13 Time building geometry restraints manager: 1.13 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: 1449 1.30 - 1.43: 2214 1.43 - 1.55: 5085 1.55 - 1.68: 9 1.68 - 1.81: 108 Bond restraints: 8865 Sorted by residual: bond pdb=" CG HIC A 73 " pdb=" CD2 HIC A 73 " ideal model delta sigma weight residual 1.369 1.305 0.064 2.00e-02 2.50e+03 1.01e+01 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 9.72e+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 9.61e+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 9.57e+00 bond pdb=" C HIC C 73 " pdb=" O HIC C 73 " ideal model delta sigma weight residual 1.231 1.170 0.061 2.00e-02 2.50e+03 9.40e+00 ... (remaining 8860 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 10985 1.70 - 3.39: 816 3.39 - 5.09: 146 5.09 - 6.78: 56 6.78 - 8.48: 39 Bond angle restraints: 12042 Sorted by residual: angle pdb=" N LYS B 118 " pdb=" CA LYS B 118 " pdb=" C LYS B 118 " ideal model delta sigma weight residual 111.82 104.11 7.71 1.16e+00 7.43e-01 4.41e+01 angle pdb=" N LYS C 118 " pdb=" CA LYS C 118 " pdb=" C LYS C 118 " ideal model delta sigma weight residual 111.82 104.15 7.67 1.16e+00 7.43e-01 4.37e+01 angle pdb=" N LYS A 118 " pdb=" CA LYS A 118 " pdb=" C LYS A 118 " ideal model delta sigma weight residual 111.82 104.16 7.66 1.16e+00 7.43e-01 4.36e+01 angle pdb=" C ALA C 131 " pdb=" CA ALA C 131 " pdb=" CB ALA C 131 " ideal model delta sigma weight residual 115.89 108.76 7.13 1.32e+00 5.74e-01 2.92e+01 angle pdb=" C ALA B 131 " pdb=" CA ALA B 131 " pdb=" CB ALA B 131 " ideal model delta sigma weight residual 115.89 108.77 7.12 1.32e+00 5.74e-01 2.91e+01 ... (remaining 12037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.63: 5097 21.63 - 43.26: 165 43.26 - 64.89: 39 64.89 - 86.53: 9 86.53 - 108.16: 6 Dihedral angle restraints: 5316 sinusoidal: 2136 harmonic: 3180 Sorted by residual: dihedral pdb=" O2A ADP B 801 " pdb=" O3A ADP B 801 " pdb=" PA ADP B 801 " pdb=" PB ADP B 801 " ideal model delta sinusoidal sigma weight residual -60.00 48.16 -108.16 1 2.00e+01 2.50e-03 3.15e+01 dihedral pdb=" O2A ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PA ADP A 801 " pdb=" PB ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 48.15 -108.15 1 2.00e+01 2.50e-03 3.15e+01 dihedral pdb=" O2A ADP C 801 " pdb=" O3A ADP C 801 " pdb=" PA ADP C 801 " pdb=" PB ADP C 801 " ideal model delta sinusoidal sigma weight residual -60.00 48.14 -108.14 1 2.00e+01 2.50e-03 3.15e+01 ... (remaining 5313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 696 0.041 - 0.082: 421 0.082 - 0.124: 158 0.124 - 0.165: 43 0.165 - 0.206: 23 Chirality restraints: 1341 Sorted by residual: chirality pdb=" CA PHE C 223 " pdb=" N PHE C 223 " pdb=" C PHE C 223 " pdb=" CB PHE C 223 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA PHE A 223 " pdb=" N PHE A 223 " pdb=" C PHE A 223 " pdb=" CB PHE A 223 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA PHE B 223 " pdb=" N PHE B 223 " pdb=" C PHE B 223 " pdb=" CB PHE B 223 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1338 not shown) Planarity restraints: 1536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 101 " 0.051 5.00e-02 4.00e+02 7.79e-02 9.70e+00 pdb=" N PRO B 102 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 102 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 102 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 101 " -0.051 5.00e-02 4.00e+02 7.78e-02 9.68e+00 pdb=" N PRO C 102 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO C 102 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 102 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 101 " 0.051 5.00e-02 4.00e+02 7.76e-02 9.64e+00 pdb=" N PRO A 102 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " 0.042 5.00e-02 4.00e+02 ... (remaining 1533 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 123 2.52 - 3.11: 8096 3.11 - 3.71: 13858 3.71 - 4.30: 19990 4.30 - 4.90: 31022 Nonbonded interactions: 73089 Sorted by model distance: nonbonded pdb=" NZ LYS A 113 " pdb=" NH2 ARG A 116 " model vdw 1.920 3.200 nonbonded pdb=" NZ LYS C 113 " pdb=" NH2 ARG C 116 " model vdw 1.920 3.200 nonbonded pdb=" NZ LYS B 113 " pdb=" NH2 ARG B 116 " model vdw 1.920 3.200 nonbonded pdb=" OG1 THR A 358 " pdb=" OE1 GLU A 361 " model vdw 2.071 3.040 nonbonded pdb=" OG1 THR C 358 " pdb=" OE1 GLU C 361 " model vdw 2.072 3.040 ... (remaining 73084 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: 0.02 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: 0.270 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.170 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 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 : 0.008 0.076 8865 Z= 0.371 Angle : 1.112 8.475 12042 Z= 0.591 Chirality : 0.062 0.206 1341 Planarity : 0.007 0.078 1536 Dihedral : 12.768 108.157 3282 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 32.31 Ramachandran Plot: Outliers : 0.37 % Allowed : 12.83 % Favored : 86.80 % Rotamer: Outliers : 0.33 % Allowed : 2.93 % Favored : 96.74 % 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: -4.62 (0.20), residues: 1068 helix: -4.23 (0.16), residues: 300 sheet: -2.44 (0.38), residues: 141 loop : -2.68 (0.21), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 254 TYR 0.024 0.004 TYR B 337 PHE 0.022 0.002 PHE B 262 TRP 0.011 0.002 TRP C 86 HIS 0.007 0.003 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00812 / 0.37 ( 8865) covalent geometry : angle 1.11208 / 0.59 (12042) hydrogen bonds : bond 0.31873 / 21.36 ( 252) hydrogen bonds : angle 11.01604 / 7.49 ( 684) *********************** 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 250 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 247 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 133 TYR cc_start: 0.8034 (t80) cc_final: 0.7321 (t80) REVERT: C 325 MET cc_start: 0.9394 (ttp) cc_final: 0.9106 (mtt) REVERT: A 315 LYS cc_start: 0.8188 (tttm) cc_final: 0.7616 (ttmm) REVERT: B 325 MET cc_start: 0.9368 (ttp) cc_final: 0.9120 (mtt) outliers start: 3 outliers final: 3 residues processed: 250 average time/residue: 0.0820 time to fit residues: 29.3159 Evaluate side-chains 143 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 140 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain B residue 224 GLU 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: 4.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 12 ASN C 87 HIS C 128 ASN C 280 ASN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 12 ASN A 87 HIS A 128 ASN A 280 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN B 49 GLN B 87 HIS B 128 ASN B 246 GLN B 280 ASN B 371 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.090705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.080769 restraints weight = 23973.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.082879 restraints weight = 11911.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.084328 restraints weight = 7087.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.085202 restraints weight = 4796.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.085932 restraints weight = 3661.542| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2648 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= 0.201 Angle : 0.886 8.240 12042 Z= 0.439 Chirality : 0.053 0.179 1341 Planarity : 0.006 0.062 1536 Dihedral : 12.422 119.477 1254 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 3.15 % Allowed : 12.16 % Favored : 84.69 % 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: -3.69 (0.23), residues: 1068 helix: -2.71 (0.22), residues: 351 sheet: -2.39 (0.32), residues: 201 loop : -2.16 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 290 TYR 0.021 0.002 TYR B 218 PHE 0.021 0.002 PHE C 352 TRP 0.013 0.002 TRP A 356 HIS 0.004 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 ( 8865) covalent geometry : angle 0.88616 / 0.44 (12042) hydrogen bonds : bond 0.05269 / 3.61 ( 252) hydrogen bonds : angle 6.63766 / 4.45 ( 684) *********************** 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 198 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 GLN cc_start: 0.7964 (pp30) cc_final: 0.7687 (pp30) REVERT: B 106 THR cc_start: 0.7583 (m) cc_final: 0.7228 (p) outliers start: 29 outliers final: 11 residues processed: 186 average time/residue: 0.0774 time to fit residues: 21.4882 Evaluate side-chains 147 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 216 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 6 optimal weight: 7.9990 chunk 16 optimal weight: 0.0270 chunk 83 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 overall best weight: 4.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 296 ASN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.091291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.081284 restraints weight = 23623.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.083383 restraints weight = 12000.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.084835 restraints weight = 7218.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.085808 restraints weight = 4939.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.086421 restraints weight = 3732.404| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8865 Z= 0.180 Angle : 0.848 11.572 12042 Z= 0.409 Chirality : 0.050 0.175 1341 Planarity : 0.006 0.057 1536 Dihedral : 10.843 124.067 1245 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.80 % Favored : 87.92 % Rotamer: Outliers : 3.58 % Allowed : 17.70 % Favored : 78.72 % 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: -3.06 (0.24), residues: 1068 helix: -1.97 (0.24), residues: 357 sheet: -2.16 (0.31), residues: 201 loop : -1.91 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 290 TYR 0.019 0.002 TYR C 218 PHE 0.014 0.002 PHE A 223 TRP 0.018 0.002 TRP B 356 HIS 0.018 0.003 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 ( 8865) covalent geometry : angle 0.84819 / 0.41 (12042) hydrogen bonds : bond 0.04040 / 2.76 ( 252) hydrogen bonds : angle 5.82613 / 3.90 ( 684) *********************** 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 190 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 119 MET cc_start: 0.8806 (tmm) cc_final: 0.8516 (tmm) REVERT: C 305 MET cc_start: 0.8375 (mmm) cc_final: 0.8171 (mmm) REVERT: A 106 THR cc_start: 0.7507 (m) cc_final: 0.7296 (p) REVERT: A 119 MET cc_start: 0.8912 (tmm) cc_final: 0.8312 (tmm) REVERT: B 313 MET cc_start: 0.8491 (mtm) cc_final: 0.8193 (ttp) outliers start: 33 outliers final: 20 residues processed: 179 average time/residue: 0.0720 time to fit residues: 19.3586 Evaluate side-chains 159 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 327 ILE 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: 8.9990 chunk 39 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 14 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 63 optimal weight: 0.0980 chunk 6 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 354 GLN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.090433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.080340 restraints weight = 24617.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.082405 restraints weight = 12480.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.083827 restraints weight = 7557.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.084726 restraints weight = 5204.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.085412 restraints weight = 3994.406| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8865 Z= 0.201 Angle : 0.831 10.115 12042 Z= 0.401 Chirality : 0.050 0.198 1341 Planarity : 0.006 0.055 1536 Dihedral : 10.617 126.600 1245 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.24 % Favored : 88.67 % Rotamer: Outliers : 4.45 % Allowed : 19.65 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.24), residues: 1068 helix: -1.57 (0.25), residues: 357 sheet: -1.89 (0.33), residues: 207 loop : -1.92 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 290 TYR 0.022 0.002 TYR C 218 PHE 0.014 0.002 PHE A 223 TRP 0.014 0.002 TRP C 356 HIS 0.024 0.002 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 ( 8865) covalent geometry : angle 0.83129 / 0.40 (12042) hydrogen bonds : bond 0.03739 / 2.54 ( 252) hydrogen bonds : angle 5.60712 / 3.76 ( 684) *********************** 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 186 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 105 LEU cc_start: 0.8697 (tp) cc_final: 0.8354 (mp) REVERT: C 119 MET cc_start: 0.8724 (tmm) cc_final: 0.8463 (tmm) REVERT: A 88 HIS cc_start: 0.7631 (OUTLIER) cc_final: 0.7405 (m-70) REVERT: A 119 MET cc_start: 0.8963 (tmm) cc_final: 0.8483 (tmm) REVERT: A 313 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8109 (ttm) REVERT: B 221 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8698 (tt) REVERT: B 313 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7686 (ttp) outliers start: 41 outliers final: 19 residues processed: 172 average time/residue: 0.0744 time to fit residues: 19.1775 Evaluate side-chains 150 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 6 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 354 GLN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 12 ASN ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.089541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.079525 restraints weight = 24382.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.081581 restraints weight = 12385.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.082993 restraints weight = 7505.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.083958 restraints weight = 5177.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.084468 restraints weight = 3925.483| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8865 Z= 0.243 Angle : 0.857 10.721 12042 Z= 0.415 Chirality : 0.051 0.197 1341 Planarity : 0.006 0.057 1536 Dihedral : 10.553 125.591 1245 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.28 % Allowed : 13.39 % Favored : 86.33 % Rotamer: Outliers : 6.08 % Allowed : 18.68 % Favored : 75.24 % 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: -2.74 (0.24), residues: 1068 helix: -1.50 (0.25), residues: 357 sheet: -1.73 (0.34), residues: 204 loop : -2.01 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 290 TYR 0.023 0.002 TYR A 218 PHE 0.013 0.002 PHE C 200 TRP 0.014 0.002 TRP B 356 HIS 0.028 0.003 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.24 ( 8865) covalent geometry : angle 0.85723 / 0.42 (12042) hydrogen bonds : bond 0.03926 / 2.66 ( 252) hydrogen bonds : angle 5.70121 / 3.83 ( 684) *********************** 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 190 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 134 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 119 MET cc_start: 0.8737 (tmm) cc_final: 0.8369 (tmm) REVERT: C 314 GLN cc_start: 0.8541 (tp40) cc_final: 0.7871 (mm-40) REVERT: C 325 MET cc_start: 0.4536 (mtt) cc_final: 0.4202 (mtt) REVERT: A 119 MET cc_start: 0.8902 (tmm) cc_final: 0.8517 (tmm) REVERT: A 313 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8203 (ttm) REVERT: B 75 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.9088 (tt) REVERT: B 221 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8712 (tt) REVERT: B 236 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8823 (pp) REVERT: B 313 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7900 (ttp) outliers start: 56 outliers final: 29 residues processed: 174 average time/residue: 0.0772 time to fit residues: 19.7569 Evaluate side-chains 154 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 87 HIS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 361 GLU 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: 5.9990 chunk 18 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 76 optimal weight: 20.0000 chunk 97 optimal weight: 0.6980 chunk 105 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.090497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.080484 restraints weight = 24280.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.082567 restraints weight = 12271.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.084004 restraints weight = 7399.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.084943 restraints weight = 5064.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.085568 restraints weight = 3838.169| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8865 Z= 0.192 Angle : 0.823 10.263 12042 Z= 0.394 Chirality : 0.049 0.190 1341 Planarity : 0.005 0.056 1536 Dihedral : 10.299 126.744 1245 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.99 % Favored : 87.73 % Rotamer: Outliers : 5.54 % Allowed : 18.13 % Favored : 76.33 % 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: -2.54 (0.25), residues: 1068 helix: -1.24 (0.26), residues: 357 sheet: -1.67 (0.35), residues: 204 loop : -1.94 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 290 TYR 0.022 0.002 TYR A 218 PHE 0.014 0.002 PHE A 223 TRP 0.020 0.002 TRP B 356 HIS 0.022 0.003 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 ( 8865) covalent geometry : angle 0.82349 / 0.39 (12042) hydrogen bonds : bond 0.03533 / 2.41 ( 252) hydrogen bonds : angle 5.56010 / 3.74 ( 684) *********************** 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 193 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 142 time to evaluate : 0.368 Fit side-chains REVERT: C 119 MET cc_start: 0.8781 (tmm) cc_final: 0.8393 (tmm) REVERT: C 199 SER cc_start: 0.8866 (t) cc_final: 0.8447 (p) REVERT: C 236 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8832 (pp) REVERT: A 88 HIS cc_start: 0.7797 (OUTLIER) cc_final: 0.7527 (m-70) REVERT: A 119 MET cc_start: 0.8857 (tmm) cc_final: 0.8447 (tmm) REVERT: A 313 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8148 (ttm) REVERT: B 236 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8830 (pp) outliers start: 51 outliers final: 32 residues processed: 174 average time/residue: 0.0775 time to fit residues: 20.1851 Evaluate side-chains 166 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 95 ARG Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 12 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 101 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 40 optimal weight: 40.0000 chunk 7 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 103 optimal weight: 0.1980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.092349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.082308 restraints weight = 24457.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.084433 restraints weight = 12165.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.085900 restraints weight = 7272.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.086876 restraints weight = 4961.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.087391 restraints weight = 3744.851| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8865 Z= 0.155 Angle : 0.806 10.668 12042 Z= 0.382 Chirality : 0.048 0.184 1341 Planarity : 0.005 0.054 1536 Dihedral : 10.090 128.520 1245 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.99 % Favored : 87.73 % Rotamer: Outliers : 4.78 % Allowed : 19.11 % Favored : 76.11 % 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 (0.25), residues: 1068 helix: -1.21 (0.26), residues: 369 sheet: -1.20 (0.38), residues: 183 loop : -1.91 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 290 TYR 0.020 0.002 TYR A 218 PHE 0.020 0.001 PHE A 223 TRP 0.019 0.002 TRP B 356 HIS 0.037 0.003 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 8865) covalent geometry : angle 0.80600 / 0.38 (12042) hydrogen bonds : bond 0.03251 / 2.23 ( 252) hydrogen bonds : angle 5.31060 / 3.58 ( 684) *********************** 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 190 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 146 time to evaluate : 0.277 Fit side-chains REVERT: C 103 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8308 (p) REVERT: C 119 MET cc_start: 0.8670 (tmm) cc_final: 0.8330 (tmm) REVERT: C 199 SER cc_start: 0.8859 (t) cc_final: 0.8452 (p) REVERT: C 314 GLN cc_start: 0.8366 (tp40) cc_final: 0.7741 (mm110) REVERT: C 352 PHE cc_start: 0.7755 (t80) cc_final: 0.7538 (t80) REVERT: A 88 HIS cc_start: 0.7829 (OUTLIER) cc_final: 0.7556 (m-70) REVERT: A 119 MET cc_start: 0.8738 (tmm) cc_final: 0.8309 (tmm) REVERT: A 137 GLN cc_start: 0.8199 (mp10) cc_final: 0.7942 (mp10) REVERT: A 313 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8211 (ttp) REVERT: A 324 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8346 (t) outliers start: 44 outliers final: 30 residues processed: 174 average time/residue: 0.0748 time to fit residues: 19.4097 Evaluate side-chains 161 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 87 HIS Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 58 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 chunk 99 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 GLN ** 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 = 0.3293 r_free = 0.3293 target = 0.092253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.082254 restraints weight = 24145.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.084374 restraints weight = 12174.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.085838 restraints weight = 7312.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.086829 restraints weight = 4984.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.087461 restraints weight = 3749.761| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8865 Z= 0.163 Angle : 0.824 10.912 12042 Z= 0.388 Chirality : 0.049 0.191 1341 Planarity : 0.005 0.053 1536 Dihedral : 10.025 128.700 1245 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.49 % Favored : 89.14 % Rotamer: Outliers : 5.21 % Allowed : 19.11 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.25), residues: 1068 helix: -1.15 (0.26), residues: 369 sheet: -1.02 (0.43), residues: 153 loop : -1.87 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 290 TYR 0.021 0.002 TYR A 218 PHE 0.017 0.002 PHE B 352 TRP 0.017 0.002 TRP B 356 HIS 0.032 0.003 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 8865) covalent geometry : angle 0.82369 / 0.39 (12042) hydrogen bonds : bond 0.03375 / 2.31 ( 252) hydrogen bonds : angle 5.27510 / 3.57 ( 684) *********************** 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 181 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 133 time to evaluate : 0.353 Fit side-chains REVERT: C 103 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8441 (p) REVERT: C 119 MET cc_start: 0.8696 (tmm) cc_final: 0.8298 (tmm) REVERT: C 199 SER cc_start: 0.8880 (t) cc_final: 0.8473 (p) REVERT: C 352 PHE cc_start: 0.7804 (t80) cc_final: 0.7549 (t80) REVERT: A 88 HIS cc_start: 0.7804 (OUTLIER) cc_final: 0.7545 (m-70) REVERT: A 119 MET cc_start: 0.8743 (tmm) cc_final: 0.8308 (tmm) REVERT: A 313 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.8055 (ttm) REVERT: A 324 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8342 (t) outliers start: 48 outliers final: 32 residues processed: 163 average time/residue: 0.0694 time to fit residues: 17.1222 Evaluate side-chains 159 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 87 HIS Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 64 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 3 optimal weight: 0.0470 chunk 28 optimal weight: 7.9990 overall best weight: 3.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.092434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.082393 restraints weight = 24104.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.084506 restraints weight = 12124.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.085927 restraints weight = 7289.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.086861 restraints weight = 5007.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.087578 restraints weight = 3817.939| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8865 Z= 0.168 Angle : 0.836 11.096 12042 Z= 0.394 Chirality : 0.049 0.183 1341 Planarity : 0.005 0.053 1536 Dihedral : 9.984 128.684 1245 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.96 % Favored : 88.76 % Rotamer: Outliers : 4.23 % Allowed : 20.96 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.24 (0.25), residues: 1068 helix: -1.17 (0.26), residues: 369 sheet: -1.09 (0.43), residues: 153 loop : -1.80 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 290 TYR 0.021 0.002 TYR A 218 PHE 0.021 0.002 PHE B 352 TRP 0.016 0.002 TRP C 356 HIS 0.040 0.003 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 8865) covalent geometry : angle 0.83564 / 0.39 (12042) hydrogen bonds : bond 0.03427 / 2.31 ( 252) hydrogen bonds : angle 5.22566 / 3.55 ( 684) *********************** 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 165 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 0.343 Fit side-chains REVERT: C 103 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8534 (p) REVERT: C 119 MET cc_start: 0.8669 (tmm) cc_final: 0.8415 (tmm) REVERT: C 199 SER cc_start: 0.8854 (t) cc_final: 0.8463 (p) REVERT: C 314 GLN cc_start: 0.8272 (tp40) cc_final: 0.7674 (mm110) REVERT: C 352 PHE cc_start: 0.7819 (t80) cc_final: 0.7592 (t80) REVERT: A 119 MET cc_start: 0.8748 (tmm) cc_final: 0.8321 (tmm) REVERT: A 313 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.8061 (ttm) REVERT: A 324 THR cc_start: 0.8616 (OUTLIER) cc_final: 0.8342 (t) outliers start: 39 outliers final: 31 residues processed: 150 average time/residue: 0.0715 time to fit residues: 16.2886 Evaluate side-chains 155 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 87 HIS Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 327 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 45 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 35 optimal weight: 20.0000 chunk 50 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 12 ASN ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 GLN ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.091798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.081833 restraints weight = 24239.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.083906 restraints weight = 12267.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.085317 restraints weight = 7429.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.086278 restraints weight = 5097.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.086869 restraints weight = 3860.804| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8865 Z= 0.186 Angle : 0.859 10.156 12042 Z= 0.407 Chirality : 0.049 0.184 1341 Planarity : 0.005 0.053 1536 Dihedral : 10.028 126.490 1245 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.89 % Favored : 87.83 % Rotamer: Outliers : 4.45 % Allowed : 21.93 % Favored : 73.62 % 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: -2.26 (0.25), residues: 1068 helix: -1.19 (0.26), residues: 369 sheet: -1.09 (0.43), residues: 153 loop : -1.82 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 290 TYR 0.022 0.002 TYR A 218 PHE 0.021 0.002 PHE B 352 TRP 0.017 0.002 TRP B 356 HIS 0.036 0.003 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 ( 8865) covalent geometry : angle 0.85936 / 0.41 (12042) hydrogen bonds : bond 0.03426 / 2.32 ( 252) hydrogen bonds : angle 5.27755 / 3.59 ( 684) ********************** 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 166 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.361 Fit side-chains REVERT: C 103 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8430 (p) REVERT: C 119 MET cc_start: 0.8689 (tmm) cc_final: 0.8420 (tmm) REVERT: C 354 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7459 (pp30) REVERT: A 88 HIS cc_start: 0.7927 (OUTLIER) cc_final: 0.7643 (m-70) REVERT: A 119 MET cc_start: 0.8774 (tmm) cc_final: 0.8290 (tmm) REVERT: A 324 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8358 (t) REVERT: B 82 MET cc_start: 0.8164 (tpt) cc_final: 0.7758 (tmm) outliers start: 41 outliers final: 33 residues processed: 153 average time/residue: 0.0748 time to fit residues: 17.2218 Evaluate side-chains 157 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 120 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 87 HIS Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 75 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 4 optimal weight: 30.0000 chunk 83 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 GLN ** 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 = 0.3283 r_free = 0.3283 target = 0.091682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.081728 restraints weight = 24162.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.083797 restraints weight = 12215.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.085196 restraints weight = 7396.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.086150 restraints weight = 5085.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.086755 restraints weight = 3859.488| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 8865 Z= 0.234 Angle : 1.136 59.197 12042 Z= 0.607 Chirality : 0.053 0.639 1341 Planarity : 0.005 0.053 1536 Dihedral : 10.035 126.462 1245 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.99 % Favored : 87.73 % Rotamer: Outliers : 4.45 % Allowed : 21.28 % Favored : 74.27 % Cbeta Deviations : 0.10 % 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: -2.24 (0.25), residues: 1068 helix: -1.20 (0.26), residues: 369 sheet: -1.08 (0.43), residues: 153 loop : -1.78 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 290 TYR 0.022 0.002 TYR A 218 PHE 0.017 0.002 PHE C 352 TRP 0.016 0.002 TRP B 356 HIS 0.049 0.003 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.23 ( 8865) covalent geometry : angle 1.13648 / 0.61 (12042) hydrogen bonds : bond 0.03448 / 2.34 ( 252) hydrogen bonds : angle 5.28007 / 3.59 ( 684) =============================================================================== Job complete usr+sys time: 1243.06 seconds wall clock time: 22 minutes 25.64 seconds (1345.64 seconds total)