Starting phenix.real_space_refine on Thu Mar 13 06:53:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6av9_7007/03_2025/6av9_7007.cif Found real_map, /net/cci-nas-00/data/ceres_data/6av9_7007/03_2025/6av9_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_7007/03_2025/6av9_7007.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6av9_7007/03_2025/6av9_7007.map" model { file = "/net/cci-nas-00/data/ceres_data/6av9_7007/03_2025/6av9_7007.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6av9_7007/03_2025/6av9_7007.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8673 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" 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: "A" 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: C, B Time building chain proxies: 5.45, per 1000 atoms: 0.63 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: 4.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.98 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: 2.44 Time building geometry restraints manager: 3.22 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.870 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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= 0.539 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 : 32.37 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.011 0.002 TRP C 86 HIS 0.007 0.003 HIS A 101 PHE 0.022 0.002 PHE B 262 TYR 0.024 0.004 TYR B 337 ARG 0.006 0.001 ARG B 254 *********************** 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 : 1.076 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: 0.9393 (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: 0.2213 time to fit residues: 77.3805 Evaluate side-chains 145 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 142 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 91 optimal weight: 0.0010 chunk 81 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 55 optimal weight: 0.0980 chunk 43 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 32 optimal weight: 0.0980 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 87 HIS ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 12 ASN A 87 HIS A 314 GLN ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN B 49 GLN B 87 HIS ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.095721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.085659 restraints weight = 23292.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.087873 restraints weight = 11548.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.089328 restraints weight = 6861.843| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8865 Z= 0.215 Angle : 0.860 7.722 12042 Z= 0.422 Chirality : 0.051 0.174 1341 Planarity : 0.006 0.058 1536 Dihedral : 12.152 122.342 1254 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 2.82 % Allowed : 12.16 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.22), residues: 1068 helix: -2.31 (0.23), residues: 345 sheet: -2.31 (0.32), residues: 204 loop : -2.06 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 356 HIS 0.006 0.001 HIS B 101 PHE 0.023 0.002 PHE C 352 TYR 0.017 0.002 TYR B 218 ARG 0.003 0.001 ARG B 254 *********************** 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 234 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 1.033 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: symmetry clash revert: symmetry clash REVERT: C 105 LEU cc_start: 0.8668 (tp) cc_final: 0.8449 (mp) REVERT: C 106 THR cc_start: 0.7722 (m) cc_final: 0.7228 (p) REVERT: C 133 TYR cc_start: 0.7713 (t80) cc_final: 0.7313 (t80) REVERT: C 176 MET cc_start: 0.8181 (mmm) cc_final: 0.7967 (mmm) REVERT: C 355 MET cc_start: 0.8096 (tpt) cc_final: 0.7750 (tpp) REVERT: A 88 HIS cc_start: 0.7441 (OUTLIER) cc_final: 0.7239 (m-70) REVERT: A 105 LEU cc_start: 0.8459 (tp) cc_final: 0.8209 (tp) REVERT: A 106 THR cc_start: 0.7688 (m) cc_final: 0.7480 (p) REVERT: A 315 LYS cc_start: 0.7772 (tttm) cc_final: 0.7474 (ttmm) REVERT: B 79 TRP cc_start: 0.8586 (m100) cc_final: 0.8167 (m100) REVERT: B 106 THR cc_start: 0.7476 (m) cc_final: 0.7184 (p) outliers start: 26 outliers final: 7 residues processed: 225 average time/residue: 0.1716 time to fit residues: 56.2185 Evaluate side-chains 164 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 156 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 95 ARG 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 2 optimal weight: 0.3980 chunk 52 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 64 optimal weight: 0.0050 chunk 42 optimal weight: 5.9990 chunk 47 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 overall best weight: 2.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN B 371 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.094627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.084432 restraints weight = 23778.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.086643 restraints weight = 11849.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.088122 restraints weight = 7070.584| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8865 Z= 0.236 Angle : 0.822 11.280 12042 Z= 0.392 Chirality : 0.049 0.177 1341 Planarity : 0.005 0.051 1536 Dihedral : 10.491 126.237 1245 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 3.04 % Allowed : 17.70 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.23), residues: 1068 helix: -1.73 (0.24), residues: 354 sheet: -2.11 (0.31), residues: 207 loop : -1.86 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 356 HIS 0.018 0.002 HIS A 101 PHE 0.013 0.002 PHE C 352 TYR 0.019 0.002 TYR B 218 ARG 0.005 0.000 ARG B 290 *********************** 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 198 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 1.265 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 119 MET cc_start: 0.9020 (tmm) cc_final: 0.8469 (tmm) REVERT: A 315 LYS cc_start: 0.8028 (tttm) cc_final: 0.7447 (ttmm) REVERT: A 324 THR cc_start: 0.8713 (p) cc_final: 0.8372 (t) REVERT: B 34 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.9055 (mp) REVERT: B 106 THR cc_start: 0.7775 (m) cc_final: 0.7521 (p) REVERT: B 221 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8684 (tt) REVERT: B 313 MET cc_start: 0.8357 (mtm) cc_final: 0.7994 (ttp) outliers start: 28 outliers final: 15 residues processed: 188 average time/residue: 0.1795 time to fit residues: 49.7253 Evaluate side-chains 166 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain B residue 34 ILE 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 203 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 221 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 30 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 72 optimal weight: 30.0000 chunk 104 optimal weight: 20.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 280 ASN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.095661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.085491 restraints weight = 23542.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.087688 restraints weight = 11728.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.089147 restraints weight = 7006.923| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8865 Z= 0.206 Angle : 0.785 9.881 12042 Z= 0.373 Chirality : 0.047 0.169 1341 Planarity : 0.005 0.048 1536 Dihedral : 10.216 128.391 1245 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.02 % Favored : 89.89 % Rotamer: Outliers : 3.37 % Allowed : 19.87 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.24), residues: 1068 helix: -1.33 (0.25), residues: 357 sheet: -1.79 (0.34), residues: 207 loop : -1.84 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 356 HIS 0.021 0.003 HIS B 101 PHE 0.008 0.001 PHE A 223 TYR 0.018 0.001 TYR C 218 ARG 0.003 0.000 ARG B 290 *********************** 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 196 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 313 MET cc_start: 0.8363 (mtm) cc_final: 0.8089 (ttp) REVERT: C 324 THR cc_start: 0.8568 (p) cc_final: 0.8262 (t) REVERT: A 82 MET cc_start: 0.8061 (tpt) cc_final: 0.7788 (tmm) REVERT: A 119 MET cc_start: 0.8963 (tmm) cc_final: 0.8430 (tmm) REVERT: A 313 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.8048 (ttp) REVERT: A 314 GLN cc_start: 0.8084 (tp40) cc_final: 0.7652 (mm-40) REVERT: A 324 THR cc_start: 0.8673 (p) cc_final: 0.8400 (t) REVERT: B 34 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.9074 (mp) REVERT: B 221 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8730 (tt) REVERT: B 313 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7706 (ttp) outliers start: 31 outliers final: 13 residues processed: 186 average time/residue: 0.2079 time to fit residues: 55.7603 Evaluate side-chains 158 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL 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 216 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain B residue 34 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 221 LEU Chi-restraints excluded: chain B residue 313 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 98 optimal weight: 0.3980 chunk 41 optimal weight: 7.9990 chunk 105 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 overall best weight: 5.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 GLN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 ASN A 296 ASN ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.091099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.081229 restraints weight = 23886.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.083258 restraints weight = 12022.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.084671 restraints weight = 7249.535| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8865 Z= 0.317 Angle : 0.830 10.185 12042 Z= 0.399 Chirality : 0.050 0.207 1341 Planarity : 0.005 0.051 1536 Dihedral : 10.221 123.783 1245 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.42 % Favored : 88.39 % Rotamer: Outliers : 4.67 % Allowed : 19.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.25), residues: 1068 helix: -1.13 (0.26), residues: 360 sheet: -1.66 (0.35), residues: 201 loop : -1.82 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 356 HIS 0.017 0.003 HIS B 101 PHE 0.018 0.002 PHE C 200 TYR 0.022 0.002 TYR C 294 ARG 0.005 0.001 ARG A 290 *********************** 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: 43 poor density : 147 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 HIS cc_start: 0.7701 (m-70) cc_final: 0.7465 (t-90) REVERT: A 119 MET cc_start: 0.9044 (tmm) cc_final: 0.8461 (tmm) REVERT: A 313 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8091 (ttp) REVERT: B 221 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8748 (tt) REVERT: B 313 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7976 (ttp) REVERT: B 355 MET cc_start: 0.8285 (tpp) cc_final: 0.8010 (tpp) outliers start: 43 outliers final: 25 residues processed: 173 average time/residue: 0.1758 time to fit residues: 44.8063 Evaluate side-chains 155 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 89 THR 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 309 ILE Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 216 LEU 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 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 203 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 260 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 7 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 73 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 chunk 76 optimal weight: 30.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 ASN ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 ASN ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN B 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.088725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.078920 restraints weight = 24285.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.080903 restraints weight = 12297.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.082259 restraints weight = 7420.742| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 8865 Z= 0.416 Angle : 0.886 9.366 12042 Z= 0.431 Chirality : 0.052 0.228 1341 Planarity : 0.006 0.054 1536 Dihedral : 10.265 122.196 1245 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.80 % Favored : 87.92 % Rotamer: Outliers : 6.08 % Allowed : 17.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.24), residues: 1068 helix: -1.33 (0.26), residues: 360 sheet: -1.38 (0.37), residues: 186 loop : -2.12 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 356 HIS 0.014 0.003 HIS B 101 PHE 0.016 0.002 PHE C 352 TYR 0.025 0.002 TYR C 218 ARG 0.006 0.001 ARG A 290 *********************** 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 187 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 131 time to evaluate : 1.226 Fit side-chains revert: symmetry clash REVERT: C 119 MET cc_start: 0.8779 (tmm) cc_final: 0.8465 (tmm) REVERT: C 236 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8812 (pp) REVERT: C 313 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8058 (ttp) REVERT: C 325 MET cc_start: 0.4256 (mtt) cc_final: 0.3931 (mtt) REVERT: A 88 HIS cc_start: 0.7883 (m-70) cc_final: 0.7574 (t-90) REVERT: A 119 MET cc_start: 0.9036 (tmm) cc_final: 0.8478 (tmm) REVERT: A 137 GLN cc_start: 0.7990 (mm110) cc_final: 0.7763 (mp10) REVERT: A 313 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8140 (ttm) REVERT: B 75 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.9113 (tt) REVERT: B 221 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8734 (tt) REVERT: B 313 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8119 (ttp) outliers start: 56 outliers final: 37 residues processed: 168 average time/residue: 0.1987 time to fit residues: 48.3510 Evaluate side-chains 166 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 123 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 86 TRP 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 236 LEU Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 203 THR 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 A residue 327 ILE Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 75 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 203 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 309 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 6 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 39 optimal weight: 0.6980 chunk 53 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 chunk 78 optimal weight: 0.9980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 ASN ** 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 = 0.3298 r_free = 0.3298 target = 0.092951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.083005 restraints weight = 23916.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.085064 restraints weight = 12030.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.086370 restraints weight = 7267.178| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8865 Z= 0.230 Angle : 0.810 10.401 12042 Z= 0.383 Chirality : 0.048 0.183 1341 Planarity : 0.005 0.053 1536 Dihedral : 9.828 124.953 1245 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.37 % Allowed : 11.33 % Favored : 88.30 % Rotamer: Outliers : 4.23 % Allowed : 20.41 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.25), residues: 1068 helix: -0.97 (0.27), residues: 360 sheet: -1.25 (0.38), residues: 186 loop : -1.96 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 356 HIS 0.010 0.002 HIS A 101 PHE 0.034 0.002 PHE C 352 TYR 0.021 0.001 TYR A 218 ARG 0.008 0.000 ARG C 290 *********************** 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 197 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 0.954 Fit side-chains REVERT: C 137 GLN cc_start: 0.8040 (mm110) cc_final: 0.7808 (mp10) REVERT: C 313 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7855 (ttp) REVERT: A 82 MET cc_start: 0.8146 (tpt) cc_final: 0.7365 (tmm) REVERT: A 119 MET cc_start: 0.8954 (tmm) cc_final: 0.8391 (tmm) REVERT: A 313 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.8025 (ttm) REVERT: A 324 THR cc_start: 0.8631 (p) cc_final: 0.8368 (t) outliers start: 39 outliers final: 26 residues processed: 178 average time/residue: 0.1730 time to fit residues: 44.4060 Evaluate side-chains 160 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 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 313 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 318 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 95 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 28 optimal weight: 4.9990 chunk 86 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.091885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.081948 restraints weight = 24310.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.083999 restraints weight = 12167.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.085428 restraints weight = 7286.031| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8865 Z= 0.277 Angle : 0.848 10.138 12042 Z= 0.403 Chirality : 0.049 0.184 1341 Planarity : 0.005 0.053 1536 Dihedral : 9.839 124.257 1245 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.58 % Favored : 89.04 % Rotamer: Outliers : 4.67 % Allowed : 20.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.25), residues: 1068 helix: -1.03 (0.26), residues: 357 sheet: -1.31 (0.39), residues: 186 loop : -1.94 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 356 HIS 0.031 0.004 HIS B 101 PHE 0.027 0.002 PHE C 352 TYR 0.023 0.002 TYR A 218 ARG 0.006 0.000 ARG C 290 *********************** 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 183 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 140 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: C 121 GLN cc_start: 0.8452 (tp40) cc_final: 0.8234 (tp40) REVERT: C 137 GLN cc_start: 0.8065 (mm110) cc_final: 0.7698 (mp10) REVERT: C 313 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7579 (ttm) REVERT: C 327 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7790 (pt) REVERT: A 88 HIS cc_start: 0.7775 (m-70) cc_final: 0.7546 (t-90) REVERT: A 119 MET cc_start: 0.8929 (tmm) cc_final: 0.8375 (tmm) REVERT: A 313 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8093 (ttp) REVERT: A 324 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8373 (t) REVERT: B 119 MET cc_start: 0.8525 (tmm) cc_final: 0.8199 (tmm) outliers start: 43 outliers final: 32 residues processed: 165 average time/residue: 0.1639 time to fit residues: 40.0225 Evaluate side-chains 164 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 86 TRP 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 313 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 203 THR 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 95 ARG Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 309 ILE 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 13 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 68 optimal weight: 0.0170 chunk 103 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 50 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 overall best weight: 1.8824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 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 = 0.3327 r_free = 0.3327 target = 0.094631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.084645 restraints weight = 23987.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.086816 restraints weight = 11995.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.088265 restraints weight = 7116.586| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8865 Z= 0.214 Angle : 0.833 10.504 12042 Z= 0.391 Chirality : 0.047 0.185 1341 Planarity : 0.005 0.053 1536 Dihedral : 9.612 123.751 1245 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.47 % Allowed : 10.30 % Favored : 89.23 % Rotamer: Outliers : 3.58 % Allowed : 21.50 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.25), residues: 1068 helix: -0.98 (0.26), residues: 366 sheet: -1.62 (0.37), residues: 201 loop : -1.75 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 356 HIS 0.027 0.003 HIS B 101 PHE 0.025 0.002 PHE C 352 TYR 0.020 0.001 TYR A 218 ARG 0.003 0.000 ARG C 290 *********************** 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 189 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 176 MET cc_start: 0.8073 (mmm) cc_final: 0.7647 (mmm) REVERT: A 119 MET cc_start: 0.8821 (tmm) cc_final: 0.8288 (tmm) REVERT: A 313 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.8054 (ttm) REVERT: A 324 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.8373 (t) REVERT: B 119 MET cc_start: 0.8436 (tmm) cc_final: 0.8084 (tmm) REVERT: B 137 GLN cc_start: 0.8438 (mp10) cc_final: 0.8117 (mp10) outliers start: 33 outliers final: 26 residues processed: 172 average time/residue: 0.1784 time to fit residues: 44.9861 Evaluate side-chains 169 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL 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 309 ILE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 313 MET 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 95 ARG 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 63 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 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** ** B 353 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 = 0.3303 r_free = 0.3303 target = 0.092643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.082724 restraints weight = 24356.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.084844 restraints weight = 12273.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.086263 restraints weight = 7375.397| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5110 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= 0.287 Angle : 0.875 9.991 12042 Z= 0.415 Chirality : 0.050 0.265 1341 Planarity : 0.005 0.053 1536 Dihedral : 9.735 122.343 1245 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.37 % Allowed : 11.05 % Favored : 88.58 % Rotamer: Outliers : 4.13 % Allowed : 21.61 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.25), residues: 1068 helix: -1.15 (0.25), residues: 384 sheet: -1.30 (0.38), residues: 186 loop : -1.89 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 356 HIS 0.027 0.004 HIS B 101 PHE 0.039 0.002 PHE B 352 TYR 0.023 0.002 TYR C 218 ARG 0.005 0.000 ARG C 290 ********************** 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 173 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 135 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: C 176 MET cc_start: 0.8133 (mmm) cc_final: 0.7800 (mmm) REVERT: C 327 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7589 (pt) REVERT: A 119 MET cc_start: 0.8818 (tmm) cc_final: 0.8292 (tmm) REVERT: A 324 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8373 (t) REVERT: B 82 MET cc_start: 0.8478 (tpt) cc_final: 0.8009 (tmm) outliers start: 38 outliers final: 31 residues processed: 155 average time/residue: 0.1649 time to fit residues: 38.0114 Evaluate side-chains 165 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL 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 163 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 64 ILE 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 151 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 216 LEU 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 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 85 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 43 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 275 HIS ** B 353 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 = 0.3342 r_free = 0.3342 target = 0.094974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.085117 restraints weight = 24062.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.087274 restraints weight = 11899.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.088755 restraints weight = 7080.769| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8865 Z= 0.238 Angle : 0.854 9.851 12042 Z= 0.401 Chirality : 0.049 0.243 1341 Planarity : 0.005 0.052 1536 Dihedral : 9.524 121.684 1245 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.67 % Favored : 88.95 % Rotamer: Outliers : 4.02 % Allowed : 21.61 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.25), residues: 1068 helix: -1.00 (0.26), residues: 390 sheet: -1.26 (0.39), residues: 186 loop : -1.83 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 356 HIS 0.025 0.003 HIS B 101 PHE 0.040 0.002 PHE B 352 TYR 0.020 0.001 TYR A 218 ARG 0.004 0.000 ARG A 290 =============================================================================== Job complete usr+sys time: 2444.84 seconds wall clock time: 44 minutes 37.58 seconds (2677.58 seconds total)