Starting phenix.real_space_refine on Fri Jul 3 02:18:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k21_36824/07_2026/8k21_36824.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k21_36824/07_2026/8k21_36824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k21_36824/07_2026/8k21_36824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k21_36824/07_2026/8k21_36824.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k21_36824/07_2026/8k21_36824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k21_36824/07_2026/8k21_36824.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 468 atoms to isotropic. 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 41 5.49 5 S 63 5.16 5 C 7148 2.51 5 N 1947 2.21 5 O 2190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11389 Number of models: 1 Model: "" Number of chains: 8 Chain: "U" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 439 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "V" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 419 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "A" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 583 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "D" Number of atoms: 2327 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 295, 2317 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 289} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 295, 2322 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 289} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 2358 Chain: "E" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2353 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 5, 'TRANS': 289} Chain: "a" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 571 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "d" Number of atoms: 2360 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 295, 2350 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 289} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 295, 2350 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 289} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 2388 Chain: "e" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2337 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 289} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 3.65, per 1000 atoms: 0.32 Number of scatterers: 11389 At special positions: 0 Unit cell: (107.8, 119.9, 129.8, 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 63 16.00 P 41 15.00 O 2190 8.00 N 1947 7.00 C 7148 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: 0.94 Conformation dependent library (CDL) restraints added in 651.6 milliseconds 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2486 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 8 sheets defined 53.7% alpha, 9.7% beta 15 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 removed outlier: 4.148A pdb=" N LYS A 16 " --> pdb=" O PRO A 12 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 17 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 22 " --> pdb=" O SER A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 51 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 100 through 110 removed outlier: 4.200A pdb=" N ARG D 106 " --> pdb=" O GLN D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 122 Processing helix chain 'D' and resid 123 through 132 Processing helix chain 'D' and resid 142 through 159 removed outlier: 3.656A pdb=" N GLN D 158 " --> pdb=" O LYS D 154 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA D 159 " --> pdb=" O GLY D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 184 Processing helix chain 'D' and resid 196 through 221 Processing helix chain 'D' and resid 238 through 243 Processing helix chain 'D' and resid 243 through 248 removed outlier: 3.968A pdb=" N THR D 248 " --> pdb=" O ASP D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 264 through 279 removed outlier: 3.556A pdb=" N VAL D 273 " --> pdb=" O LYS D 269 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE D 276 " --> pdb=" O CYS D 272 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN D 279 " --> pdb=" O TYR D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.928A pdb=" N LEU D 285 " --> pdb=" O ILE D 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 66 Processing helix chain 'E' and resid 98 through 109 Processing helix chain 'E' and resid 110 through 123 Processing helix chain 'E' and resid 123 through 132 removed outlier: 4.457A pdb=" N ASP E 127 " --> pdb=" O LYS E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 156 removed outlier: 3.622A pdb=" N SER E 146 " --> pdb=" O ASN E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 184 removed outlier: 3.704A pdb=" N LYS E 178 " --> pdb=" O LYS E 174 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR E 184 " --> pdb=" O TYR E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 219 removed outlier: 3.602A pdb=" N ILE E 212 " --> pdb=" O TYR E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 248 removed outlier: 3.648A pdb=" N PHE E 240 " --> pdb=" O GLY E 236 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE E 245 " --> pdb=" O ASP E 241 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ILE E 246 " --> pdb=" O VAL E 242 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR E 248 " --> pdb=" O ASP E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 261 Processing helix chain 'E' and resid 264 through 279 removed outlier: 3.797A pdb=" N ASN E 279 " --> pdb=" O TYR E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'a' and resid 10 through 22 removed outlier: 4.447A pdb=" N LYS a 16 " --> pdb=" O PRO a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 40 through 51 Processing helix chain 'd' and resid 6 through 10 Processing helix chain 'd' and resid 58 through 68 Processing helix chain 'd' and resid 100 through 110 removed outlier: 4.280A pdb=" N ARG d 106 " --> pdb=" O GLN d 102 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP d 110 " --> pdb=" O ARG d 106 " (cutoff:3.500A) Processing helix chain 'd' and resid 110 through 132 removed outlier: 4.538A pdb=" N ARG d 125 " --> pdb=" O ILE d 121 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL d 126 " --> pdb=" O LEU d 122 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER d 130 " --> pdb=" O VAL d 126 " (cutoff:3.500A) Processing helix chain 'd' and resid 143 through 158 Processing helix chain 'd' and resid 161 through 184 Processing helix chain 'd' and resid 196 through 221 Processing helix chain 'd' and resid 238 through 243 Processing helix chain 'd' and resid 244 through 249 removed outlier: 3.760A pdb=" N SER d 249 " --> pdb=" O ILE d 245 " (cutoff:3.500A) Processing helix chain 'd' and resid 250 through 261 removed outlier: 3.636A pdb=" N LEU d 254 " --> pdb=" O ILE d 250 " (cutoff:3.500A) Processing helix chain 'd' and resid 264 through 279 Processing helix chain 'd' and resid 280 through 294 removed outlier: 3.568A pdb=" N LYS d 290 " --> pdb=" O ILE d 286 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG d 291 " --> pdb=" O ASN d 287 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU d 292 " --> pdb=" O ASN d 288 " (cutoff:3.500A) Processing helix chain 'e' and resid 58 through 68 removed outlier: 3.672A pdb=" N MET e 63 " --> pdb=" O GLU e 59 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA e 66 " --> pdb=" O SER e 62 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN e 67 " --> pdb=" O MET e 63 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY e 68 " --> pdb=" O LEU e 64 " (cutoff:3.500A) Processing helix chain 'e' and resid 98 through 110 removed outlier: 3.541A pdb=" N ASN e 103 " --> pdb=" O LYS e 99 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP e 104 " --> pdb=" O TYR e 100 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP e 110 " --> pdb=" O ARG e 106 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 132 removed outlier: 4.057A pdb=" N VAL e 126 " --> pdb=" O LEU e 122 " (cutoff:3.500A) Processing helix chain 'e' and resid 142 through 157 removed outlier: 3.932A pdb=" N ILE e 148 " --> pdb=" O ARG e 144 " (cutoff:3.500A) Processing helix chain 'e' and resid 161 through 184 Processing helix chain 'e' and resid 196 through 221 removed outlier: 3.682A pdb=" N TYR e 208 " --> pdb=" O LEU e 204 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA e 213 " --> pdb=" O ALA e 209 " (cutoff:3.500A) Processing helix chain 'e' and resid 236 through 244 removed outlier: 4.171A pdb=" N PHE e 240 " --> pdb=" O GLY e 236 " (cutoff:3.500A) Processing helix chain 'e' and resid 250 through 261 Processing helix chain 'e' and resid 264 through 279 Processing helix chain 'e' and resid 280 through 294 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 36 Processing sheet with id=AA2, first strand: chain 'D' and resid 14 through 16 removed outlier: 6.868A pdb=" N TYR D 14 " --> pdb=" O GLY D 49 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA E 83 " --> pdb=" O TRP E 73 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE E 48 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N THR E 74 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LEU E 50 " --> pdb=" O THR E 74 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASN E 12 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLY E 49 " --> pdb=" O ASN E 12 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N TYR E 14 " --> pdb=" O GLY E 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 37 through 40 removed outlier: 4.574A pdb=" N VAL D 28 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER D 55 " --> pdb=" O CYS D 19 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL D 23 " --> pdb=" O THR D 57 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE D 56 " --> pdb=" O ILE E 56 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL E 21 " --> pdb=" O THR E 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 23 through 24 removed outlier: 3.585A pdb=" N GLN E 27 " --> pdb=" O LYS E 24 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 32 through 36 removed outlier: 3.720A pdb=" N ARG a 4 " --> pdb=" O ASN a 61 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL a 58 " --> pdb=" O ALA a 69 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA a 69 " --> pdb=" O VAL a 58 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N CYS a 60 " --> pdb=" O LEU a 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'd' and resid 21 through 24 removed outlier: 3.503A pdb=" N GLN d 27 " --> pdb=" O LYS d 24 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'd' and resid 47 through 50 removed outlier: 3.673A pdb=" N PHE d 72 " --> pdb=" O ILE d 48 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA e 83 " --> pdb=" O TRP e 73 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE e 48 " --> pdb=" O PHE e 72 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N THR e 74 " --> pdb=" O ILE e 48 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU e 50 " --> pdb=" O THR e 74 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N TYR e 14 " --> pdb=" O GLY e 49 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET e 13 " --> pdb=" O ILE e 5 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'd' and resid 55 through 57 removed outlier: 3.605A pdb=" N SER e 55 " --> pdb=" O CYS e 19 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR e 57 " --> pdb=" O VAL e 21 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N VAL e 23 " --> pdb=" O THR e 57 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS e 30 " --> pdb=" O TYR e 38 " (cutoff:3.500A) 544 hydrogen bonds defined for protein. 1604 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 2.06 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1804 1.31 - 1.44: 3432 1.44 - 1.56: 6286 1.56 - 1.69: 87 1.69 - 1.82: 102 Bond restraints: 11711 Sorted by residual: bond pdb=" N PHE d 226 " pdb=" CA PHE d 226 " ideal model delta sigma weight residual 1.464 1.378 0.085 1.09e-02 8.42e+03 6.10e+01 bond pdb=" CA ASN d 224 " pdb=" C ASN d 224 " ideal model delta sigma weight residual 1.522 1.421 0.101 1.32e-02 5.74e+03 5.86e+01 bond pdb=" CA ALA d 219 " pdb=" C ALA d 219 " ideal model delta sigma weight residual 1.522 1.420 0.102 1.40e-02 5.10e+03 5.32e+01 bond pdb=" CA ALA D 118 " pdb=" C ALA D 118 " ideal model delta sigma weight residual 1.524 1.430 0.094 1.29e-02 6.01e+03 5.29e+01 bond pdb=" CA VAL d 239 " pdb=" C VAL d 239 " ideal model delta sigma weight residual 1.524 1.437 0.087 1.22e-02 6.72e+03 5.07e+01 ... (remaining 11706 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 15327 2.83 - 5.66: 534 5.66 - 8.49: 114 8.49 - 11.32: 19 11.32 - 14.15: 6 Bond angle restraints: 16000 Sorted by residual: angle pdb=" N ALA D 118 " pdb=" CA ALA D 118 " pdb=" C ALA D 118 " ideal model delta sigma weight residual 111.36 99.78 11.58 1.09e+00 8.42e-01 1.13e+02 angle pdb=" N ASN d 224 " pdb=" CA ASN d 224 " pdb=" C ASN d 224 " ideal model delta sigma weight residual 113.50 101.30 12.20 1.23e+00 6.61e-01 9.83e+01 angle pdb=" N LEU d 238 " pdb=" CA LEU d 238 " pdb=" C LEU d 238 " ideal model delta sigma weight residual 113.23 102.53 10.70 1.24e+00 6.50e-01 7.45e+01 angle pdb=" N VAL D 273 " pdb=" CA VAL D 273 " pdb=" C VAL D 273 " ideal model delta sigma weight residual 111.90 105.24 6.66 8.10e-01 1.52e+00 6.76e+01 angle pdb=" N HIS E 257 " pdb=" CA HIS E 257 " pdb=" C HIS E 257 " ideal model delta sigma weight residual 112.23 102.12 10.11 1.26e+00 6.30e-01 6.44e+01 ... (remaining 15995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5283 17.94 - 35.89: 985 35.89 - 53.83: 454 53.83 - 71.77: 107 71.77 - 89.71: 24 Dihedral angle restraints: 6853 sinusoidal: 2972 harmonic: 3881 Sorted by residual: dihedral pdb=" CA THR e 45 " pdb=" C THR e 45 " pdb=" N VAL e 46 " pdb=" CA VAL e 46 " ideal model delta harmonic sigma weight residual 180.00 153.28 26.72 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA SER d 175 " pdb=" C SER d 175 " pdb=" N LEU d 176 " pdb=" CA LEU d 176 " ideal model delta harmonic sigma weight residual 180.00 154.98 25.02 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA PHE E 188 " pdb=" C PHE E 188 " pdb=" N LYS E 189 " pdb=" CA LYS E 189 " ideal model delta harmonic sigma weight residual 180.00 155.20 24.80 0 5.00e+00 4.00e-02 2.46e+01 ... (remaining 6850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1490 0.097 - 0.194: 236 0.194 - 0.291: 42 0.291 - 0.388: 12 0.388 - 0.485: 2 Chirality restraints: 1782 Sorted by residual: chirality pdb=" CB ILE D 245 " pdb=" CA ILE D 245 " pdb=" CG1 ILE D 245 " pdb=" CG2 ILE D 245 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.88e+00 chirality pdb=" CB VAL e 105 " pdb=" CA VAL e 105 " pdb=" CG1 VAL e 105 " pdb=" CG2 VAL e 105 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" CA ILE d 251 " pdb=" N ILE d 251 " pdb=" C ILE d 251 " pdb=" CB ILE d 251 " both_signs ideal model delta sigma weight residual False 2.43 2.05 0.38 2.00e-01 2.50e+01 3.60e+00 ... (remaining 1779 not shown) Planarity restraints: 1878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 255 " -0.025 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C ALA E 255 " 0.089 2.00e-02 2.50e+03 pdb=" O ALA E 255 " -0.035 2.00e-02 2.50e+03 pdb=" N PHE E 256 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA d 209 " -0.023 2.00e-02 2.50e+03 4.68e-02 2.19e+01 pdb=" C ALA d 209 " 0.081 2.00e-02 2.50e+03 pdb=" O ALA d 209 " -0.030 2.00e-02 2.50e+03 pdb=" N TYR d 210 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 268 " 0.024 2.00e-02 2.50e+03 2.77e-02 1.35e+01 pdb=" CG PHE E 268 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 PHE E 268 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE E 268 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE E 268 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE E 268 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE E 268 " 0.003 2.00e-02 2.50e+03 ... (remaining 1875 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2126 2.77 - 3.30: 10428 3.30 - 3.83: 21040 3.83 - 4.37: 24563 4.37 - 4.90: 39521 Nonbonded interactions: 97678 Sorted by model distance: nonbonded pdb=" O THR d 171 " pdb=" OG SER d 175 " model vdw 2.232 3.040 nonbonded pdb=" O ASP e 153 " pdb=" OG1 THR e 157 " model vdw 2.251 3.040 nonbonded pdb=" OD1 ASP d 127 " pdb=" OH TYR d 284 " model vdw 2.252 3.040 nonbonded pdb=" O ASP d 153 " pdb=" OG1 THR d 157 " model vdw 2.258 3.040 nonbonded pdb=" O SER D 225 " pdb=" OG SER D 225 " model vdw 2.264 3.040 ... (remaining 97673 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 9 or (resid 10 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 14 or (resid 15 and (name \ N or name CA or name C or name O or name CB )) or resid 16 through 75)) selection = chain 'a' } ncs_group { reference = (chain 'D' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 74 or (resid 75 and (name N or name \ CA or name C or name O or name CB )) or resid 76 through 141 or (resid 142 and \ (name N or name CA or name C or name O or name CB )) or resid 143 through 149 or \ resid 151 through 234 or (resid 235 and (name N or name CA or name C or name O \ or name CB )) or resid 236 through 286 or resid 288 through 295)) selection = (chain 'E' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 74 or (resid 75 and (name N or name \ CA or name C or name O or name CB )) or resid 76 through 78 or (resid 79 throug \ h 84 and (name N or name CA or name C or name O or name CB )) or resid 85 throug \ h 110 or (resid 111 and (name N or name CA or name C or name O or name CB )) or \ resid 112 or (resid 113 and (name N or name CA or name C or name O or name CB )) \ or resid 114 through 118 or (resid 119 and (name N or name CA or name C or name \ O or name CB )) or resid 120 through 141 or (resid 142 and (name N or name CA o \ r name C or name O or name CB )) or resid 143 through 149 or resid 151 through 2 \ 34 or (resid 235 and (name N or name CA or name C or name O or name CB )) or res \ id 236 through 286 or resid 288 through 295)) selection = (chain 'd' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 74 or (resid 75 and (name N or name \ CA or name C or name O or name CB )) or resid 76 through 78 or (resid 79 throug \ h 84 and (name N or name CA or name C or name O or name CB )) or resid 85 throug \ h 110 or (resid 111 and (name N or name CA or name C or name O or name CB )) or \ resid 112 or (resid 113 and (name N or name CA or name C or name O or name CB )) \ or resid 114 through 118 or (resid 119 and (name N or name CA or name C or name \ O or name CB )) or resid 120 through 149 or resid 151 through 234 or (resid 235 \ and (name N or name CA or name C or name O or name CB )) or resid 236 through 2 \ 86 or resid 288 through 295)) selection = (chain 'e' and (resid 1 through 78 or (resid 79 through 84 and (name N or name C \ A or name C or name O or name CB )) or resid 85 through 110 or (resid 111 and (n \ ame N or name CA or name C or name O or name CB )) or resid 112 or (resid 113 an \ d (name N or name CA or name C or name O or name CB )) or resid 114 through 118 \ or (resid 119 and (name N or name CA or name C or name O or name CB )) or resid \ 120 through 141 or (resid 142 and (name N or name CA or name C or name O or name \ CB )) or resid 143 through 149 or resid 151 through 286 or resid 288 through 29 \ 5)) } 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=0.15 max=1.00 mean=1.00 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.020 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.930 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.102 11711 Z= 0.583 Angle : 1.302 14.150 16000 Z= 0.824 Chirality : 0.079 0.485 1782 Planarity : 0.008 0.112 1878 Dihedral : 22.880 89.714 4367 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.61 % Allowed : 6.91 % Favored : 92.48 % Rotamer: Outliers : 8.12 % Allowed : 36.28 % Favored : 55.60 % Cbeta Deviations : 0.08 % 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: -3.31 (0.19), residues: 1321 helix: -1.77 (0.16), residues: 685 sheet: -1.71 (0.48), residues: 111 loop : -2.76 (0.23), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG d 125 TYR 0.045 0.004 TYR d 100 PHE 0.064 0.004 PHE E 268 TRP 0.024 0.003 TRP d 218 HIS 0.014 0.002 HIS D 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00915 / 0.58 (11711) covalent geometry : angle 1.30241 / 0.82 (16000) hydrogen bonds : bond 0.17037 / 18.34 ( 580) hydrogen bonds : angle 7.33930 / 8.71 ( 1676) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 261 time to evaluate : 0.427 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.7258 (tt0) cc_final: 0.6779 (tt0) REVERT: E 260 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.8295 (m-30) REVERT: a 48 LYS cc_start: 0.8648 (mtpp) cc_final: 0.8326 (mttp) REVERT: d 228 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8806 (tp) REVERT: e 61 MET cc_start: 0.8323 (ttm) cc_final: 0.7781 (ttm) outliers start: 91 outliers final: 14 residues processed: 322 average time/residue: 0.1272 time to fit residues: 54.9104 Evaluate side-chains 159 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain E residue 125 ARG Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 261 GLN Chi-restraints excluded: chain d residue 61 MET Chi-restraints excluded: chain d residue 138 VAL Chi-restraints excluded: chain d residue 194 SER Chi-restraints excluded: chain d residue 228 LEU Chi-restraints excluded: chain d residue 233 THR Chi-restraints excluded: chain d residue 244 ASP Chi-restraints excluded: chain d residue 248 THR Chi-restraints excluded: chain e residue 27 GLN Chi-restraints excluded: chain e residue 242 VAL Chi-restraints excluded: chain e residue 294 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.0060 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 142 ASN D 150 ASN B D 168 HIS D 192 HIS D 230 HIS D 257 HIS D 279 ASN E 9 GLN E 44 ASN E 132 HIS ** E 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 GLN a 72 ASN d 199 ASN e 27 GLN e 287 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.045791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.035161 restraints weight = 132491.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.036817 restraints weight = 55500.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.037962 restraints weight = 32463.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.038727 restraints weight = 22590.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.039234 restraints weight = 17610.965| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11711 Z= 0.188 Angle : 0.813 10.813 16000 Z= 0.439 Chirality : 0.049 0.209 1782 Planarity : 0.005 0.056 1878 Dihedral : 19.302 89.703 1951 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.39 % Favored : 94.46 % Rotamer: Outliers : 4.85 % Allowed : 33.63 % Favored : 61.52 % 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: -2.09 (0.21), residues: 1321 helix: -0.52 (0.18), residues: 684 sheet: -1.46 (0.51), residues: 104 loop : -2.48 (0.23), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG d 18 TYR 0.023 0.002 TYR d 284 PHE 0.024 0.002 PHE e 152 TRP 0.017 0.002 TRP e 218 HIS 0.013 0.002 HIS e 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 (11711) covalent geometry : angle 0.81301 / 0.44 (16000) hydrogen bonds : bond 0.04877 / 5.34 ( 580) hydrogen bonds : angle 5.21874 / 6.22 ( 1676) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 149 time to evaluate : 0.457 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.7979 (tt0) cc_final: 0.7441 (tt0) REVERT: A 40 GLN cc_start: 0.8383 (tp40) cc_final: 0.8091 (tp-100) REVERT: D 101 MET cc_start: 0.8491 (mmt) cc_final: 0.8174 (tpt) REVERT: D 202 LEU cc_start: 0.9698 (OUTLIER) cc_final: 0.9302 (tp) REVERT: e 61 MET cc_start: 0.8835 (ttm) cc_final: 0.8460 (ttm) outliers start: 54 outliers final: 23 residues processed: 186 average time/residue: 0.0961 time to fit residues: 25.9972 Evaluate side-chains 148 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 276 PHE Chi-restraints excluded: chain a residue 25 LEU Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 45 THR Chi-restraints excluded: chain d residue 233 THR Chi-restraints excluded: chain d residue 244 ASP Chi-restraints excluded: chain d residue 248 THR Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 20 LYS Chi-restraints excluded: chain e residue 57 THR Chi-restraints excluded: chain e residue 183 GLU Chi-restraints excluded: chain e residue 192 HIS Chi-restraints excluded: chain e residue 266 THR Chi-restraints excluded: chain e residue 289 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 29 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 113 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 ASN D 158 GLN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.043749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.033214 restraints weight = 154121.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.034873 restraints weight = 60200.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.036024 restraints weight = 34259.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.036786 restraints weight = 23373.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.037322 restraints weight = 17943.305| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11711 Z= 0.202 Angle : 0.747 10.696 16000 Z= 0.402 Chirality : 0.046 0.195 1782 Planarity : 0.005 0.051 1878 Dihedral : 19.015 83.534 1922 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.47 % Favored : 94.46 % Rotamer: Outliers : 4.50 % Allowed : 31.77 % Favored : 63.72 % 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: -1.44 (0.22), residues: 1321 helix: 0.14 (0.19), residues: 688 sheet: -1.71 (0.46), residues: 117 loop : -2.26 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG d 18 TYR 0.018 0.002 TYR d 284 PHE 0.029 0.002 PHE E 276 TRP 0.009 0.002 TRP D 218 HIS 0.008 0.001 HIS d 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 (11711) covalent geometry : angle 0.74665 / 0.40 (16000) hydrogen bonds : bond 0.04284 / 4.78 ( 580) hydrogen bonds : angle 4.84856 / 5.79 ( 1676) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 121 time to evaluate : 0.416 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: A 34 GLU cc_start: 0.8069 (tt0) cc_final: 0.7776 (tt0) REVERT: A 40 GLN cc_start: 0.8455 (tp40) cc_final: 0.8100 (tp-100) REVERT: D 169 GLU cc_start: 0.9414 (OUTLIER) cc_final: 0.8874 (pp20) REVERT: D 202 LEU cc_start: 0.9719 (OUTLIER) cc_final: 0.9332 (tp) REVERT: a 20 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8106 (mt-10) REVERT: e 10 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8191 (pttm) REVERT: e 30 HIS cc_start: 0.7994 (OUTLIER) cc_final: 0.7144 (m170) REVERT: e 61 MET cc_start: 0.8853 (ttm) cc_final: 0.8482 (ttm) REVERT: e 106 ARG cc_start: 0.9118 (mmt90) cc_final: 0.8591 (mmt90) REVERT: e 178 LYS cc_start: 0.8463 (pttt) cc_final: 0.8206 (pttt) outliers start: 50 outliers final: 27 residues processed: 155 average time/residue: 0.0987 time to fit residues: 22.2523 Evaluate side-chains 136 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain D residue 293 CYS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 276 PHE Chi-restraints excluded: chain a residue 43 SER Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 45 THR Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain d residue 233 THR Chi-restraints excluded: chain d residue 244 ASP Chi-restraints excluded: chain d residue 248 THR Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 10 LYS Chi-restraints excluded: chain e residue 20 LYS Chi-restraints excluded: chain e residue 30 HIS Chi-restraints excluded: chain e residue 57 THR Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 192 HIS Chi-restraints excluded: chain e residue 266 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 1 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 36 HIS a 72 ASN d 89 HIS d 134 HIS d 150 ASN B ** d 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.042706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.032514 restraints weight = 144208.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.034059 restraints weight = 59555.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.035128 restraints weight = 34826.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.035850 restraints weight = 24295.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.036343 restraints weight = 18936.728| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11711 Z= 0.245 Angle : 0.738 10.062 16000 Z= 0.394 Chirality : 0.047 0.267 1782 Planarity : 0.004 0.043 1878 Dihedral : 18.960 84.012 1922 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.47 % Favored : 94.38 % Rotamer: Outliers : 4.68 % Allowed : 30.71 % Favored : 64.61 % 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: -1.09 (0.23), residues: 1321 helix: 0.46 (0.20), residues: 694 sheet: -1.99 (0.43), residues: 136 loop : -2.04 (0.25), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 190 TYR 0.022 0.002 TYR a 62 PHE 0.026 0.002 PHE E 276 TRP 0.010 0.002 TRP D 218 HIS 0.007 0.001 HIS d 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.24 (11711) covalent geometry : angle 0.73822 / 0.39 (16000) hydrogen bonds : bond 0.04202 / 4.65 ( 580) hydrogen bonds : angle 4.73104 / 5.68 ( 1676) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 104 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.7954 (tt0) cc_final: 0.7701 (tt0) REVERT: A 40 GLN cc_start: 0.8490 (tp40) cc_final: 0.8238 (tp-100) REVERT: A 54 LYS cc_start: 0.8914 (ttmt) cc_final: 0.8523 (tmtt) REVERT: D 13 MET cc_start: 0.7778 (mtm) cc_final: 0.7474 (mtm) REVERT: D 63 MET cc_start: 0.9180 (ttm) cc_final: 0.8952 (mtp) REVERT: D 169 GLU cc_start: 0.9324 (OUTLIER) cc_final: 0.8870 (pp20) REVERT: D 202 LEU cc_start: 0.9737 (OUTLIER) cc_final: 0.9327 (tp) REVERT: E 192 HIS cc_start: 0.8546 (p90) cc_final: 0.8197 (p90) REVERT: E 263 MET cc_start: 0.8911 (pmm) cc_final: 0.8649 (pmm) REVERT: a 20 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7946 (mt-10) REVERT: a 43 SER cc_start: 0.9509 (OUTLIER) cc_final: 0.9205 (p) REVERT: e 30 HIS cc_start: 0.8185 (OUTLIER) cc_final: 0.7246 (m170) REVERT: e 61 MET cc_start: 0.8858 (ttm) cc_final: 0.8562 (ttm) REVERT: e 106 ARG cc_start: 0.9120 (mmt90) cc_final: 0.8777 (mmt-90) REVERT: e 178 LYS cc_start: 0.8452 (pttt) cc_final: 0.8190 (pttt) outliers start: 52 outliers final: 28 residues processed: 144 average time/residue: 0.0848 time to fit residues: 18.3095 Evaluate side-chains 128 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain D residue 293 CYS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain a residue 25 LEU Chi-restraints excluded: chain a residue 43 SER Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 45 THR Chi-restraints excluded: chain d residue 233 THR Chi-restraints excluded: chain d residue 244 ASP Chi-restraints excluded: chain d residue 248 THR Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 20 LYS Chi-restraints excluded: chain e residue 30 HIS Chi-restraints excluded: chain e residue 34 ASP Chi-restraints excluded: chain e residue 57 THR Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 192 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 115 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 53 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN E 58 ASN ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 40 GLN ** d 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 168 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 = 0.3142 r_free = 0.3142 target = 0.043863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.032900 restraints weight = 172454.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.034619 restraints weight = 64299.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.035810 restraints weight = 36483.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.036603 restraints weight = 24988.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.037122 restraints weight = 19309.432| |-----------------------------------------------------------------------------| r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11711 Z= 0.144 Angle : 0.685 11.488 16000 Z= 0.362 Chirality : 0.045 0.232 1782 Planarity : 0.004 0.045 1878 Dihedral : 18.891 83.924 1922 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.39 % Favored : 94.53 % Rotamer: Outliers : 3.88 % Allowed : 29.39 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.23), residues: 1321 helix: 0.56 (0.20), residues: 694 sheet: -1.95 (0.43), residues: 136 loop : -1.97 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG d 18 TYR 0.022 0.002 TYR E 14 PHE 0.022 0.002 PHE A 68 TRP 0.012 0.002 TRP D 218 HIS 0.008 0.001 HIS d 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (11711) covalent geometry : angle 0.68498 / 0.36 (16000) hydrogen bonds : bond 0.03785 / 4.17 ( 580) hydrogen bonds : angle 4.54532 / 5.45 ( 1676) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 108 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.9798 (mt) cc_final: 0.9540 (tp) REVERT: A 34 GLU cc_start: 0.7899 (tt0) cc_final: 0.7632 (tt0) REVERT: A 40 GLN cc_start: 0.8528 (tp40) cc_final: 0.8234 (tp-100) REVERT: D 13 MET cc_start: 0.7615 (mtm) cc_final: 0.7392 (mtm) REVERT: D 169 GLU cc_start: 0.9325 (OUTLIER) cc_final: 0.8885 (pp20) REVERT: D 202 LEU cc_start: 0.9712 (OUTLIER) cc_final: 0.9297 (tp) REVERT: E 61 MET cc_start: 0.9311 (mmm) cc_final: 0.8881 (tpp) REVERT: E 63 MET cc_start: 0.8643 (ptm) cc_final: 0.8335 (tmm) REVERT: E 124 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8440 (mtt) REVERT: E 192 HIS cc_start: 0.8501 (p90) cc_final: 0.8138 (p90) REVERT: a 43 SER cc_start: 0.9496 (OUTLIER) cc_final: 0.9271 (p) REVERT: d 64 LEU cc_start: 0.9615 (mt) cc_final: 0.9388 (mp) REVERT: e 30 HIS cc_start: 0.8050 (OUTLIER) cc_final: 0.7083 (m170) REVERT: e 61 MET cc_start: 0.8841 (ttm) cc_final: 0.8572 (ttm) REVERT: e 106 ARG cc_start: 0.9160 (mmt90) cc_final: 0.8776 (mmt-90) REVERT: e 124 MET cc_start: 0.9134 (ptp) cc_final: 0.8894 (ptp) REVERT: e 178 LYS cc_start: 0.8305 (pttt) cc_final: 0.7981 (pttt) outliers start: 43 outliers final: 25 residues processed: 139 average time/residue: 0.0965 time to fit residues: 19.5848 Evaluate side-chains 124 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain E residue 36 ASN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain a residue 43 SER Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 140 VAL Chi-restraints excluded: chain d residue 233 THR Chi-restraints excluded: chain d residue 244 ASP Chi-restraints excluded: chain d residue 248 THR Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 30 HIS Chi-restraints excluded: chain e residue 34 ASP Chi-restraints excluded: chain e residue 57 THR Chi-restraints excluded: chain e residue 116 SER Chi-restraints excluded: chain e residue 192 HIS Chi-restraints excluded: chain e residue 256 PHE Chi-restraints excluded: chain e residue 266 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 63 optimal weight: 0.3980 chunk 108 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN ** d 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 168 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 = 0.3122 r_free = 0.3122 target = 0.043147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.033120 restraints weight = 120914.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.034618 restraints weight = 53545.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.035641 restraints weight = 32310.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.036333 restraints weight = 23034.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.036798 restraints weight = 18211.166| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11711 Z= 0.169 Angle : 0.687 11.065 16000 Z= 0.365 Chirality : 0.045 0.170 1782 Planarity : 0.004 0.044 1878 Dihedral : 18.802 83.642 1922 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.47 % Favored : 94.46 % Rotamer: Outliers : 3.88 % Allowed : 30.01 % Favored : 66.11 % 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: -0.89 (0.23), residues: 1321 helix: 0.65 (0.20), residues: 695 sheet: -1.93 (0.44), residues: 136 loop : -1.97 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG e 291 TYR 0.015 0.002 TYR a 62 PHE 0.023 0.002 PHE E 152 TRP 0.010 0.002 TRP D 218 HIS 0.007 0.001 HIS d 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (11711) covalent geometry : angle 0.68664 / 0.36 (16000) hydrogen bonds : bond 0.03780 / 4.18 ( 580) hydrogen bonds : angle 4.50886 / 5.41 ( 1676) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 103 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.9786 (mt) cc_final: 0.9517 (tp) REVERT: A 34 GLU cc_start: 0.7873 (tt0) cc_final: 0.7591 (tt0) REVERT: A 40 GLN cc_start: 0.8584 (tp40) cc_final: 0.8243 (tp-100) REVERT: D 13 MET cc_start: 0.7618 (mtm) cc_final: 0.7408 (mtm) REVERT: D 169 GLU cc_start: 0.9303 (OUTLIER) cc_final: 0.8763 (pp20) REVERT: D 202 LEU cc_start: 0.9713 (OUTLIER) cc_final: 0.9310 (tp) REVERT: E 63 MET cc_start: 0.8635 (ptm) cc_final: 0.8327 (tmm) REVERT: E 124 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8513 (mtt) REVERT: E 192 HIS cc_start: 0.8484 (p90) cc_final: 0.8100 (p90) REVERT: E 263 MET cc_start: 0.8846 (pmm) cc_final: 0.8503 (pmm) REVERT: a 43 SER cc_start: 0.9531 (OUTLIER) cc_final: 0.9286 (p) REVERT: e 30 HIS cc_start: 0.8086 (OUTLIER) cc_final: 0.7151 (m170) REVERT: e 61 MET cc_start: 0.8891 (ttm) cc_final: 0.8605 (ttm) REVERT: e 106 ARG cc_start: 0.9183 (mmt90) cc_final: 0.8768 (mmt-90) REVERT: e 171 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8623 (p) REVERT: e 178 LYS cc_start: 0.8414 (pttt) cc_final: 0.8065 (pttt) REVERT: e 263 MET cc_start: 0.8606 (ttp) cc_final: 0.7788 (ppp) outliers start: 43 outliers final: 26 residues processed: 138 average time/residue: 0.0988 time to fit residues: 20.0390 Evaluate side-chains 124 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 36 ASN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain a residue 43 SER Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 81 MET Chi-restraints excluded: chain d residue 140 VAL Chi-restraints excluded: chain d residue 233 THR Chi-restraints excluded: chain d residue 248 THR Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 30 HIS Chi-restraints excluded: chain e residue 34 ASP Chi-restraints excluded: chain e residue 57 THR Chi-restraints excluded: chain e residue 99 LYS Chi-restraints excluded: chain e residue 171 THR Chi-restraints excluded: chain e residue 180 TYR Chi-restraints excluded: chain e residue 192 HIS Chi-restraints excluded: chain e residue 256 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 39 optimal weight: 0.7980 chunk 41 optimal weight: 0.2980 chunk 90 optimal weight: 7.9990 chunk 133 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 129 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 118 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.043434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.032802 restraints weight = 167573.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.034467 restraints weight = 63782.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.035613 restraints weight = 36275.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.036387 restraints weight = 24871.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.036789 restraints weight = 19187.009| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11711 Z= 0.143 Angle : 0.691 12.713 16000 Z= 0.363 Chirality : 0.045 0.248 1782 Planarity : 0.004 0.045 1878 Dihedral : 18.694 83.515 1920 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.54 % Favored : 94.38 % Rotamer: Outliers : 3.18 % Allowed : 30.36 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.23), residues: 1321 helix: 0.70 (0.20), residues: 698 sheet: -1.75 (0.46), residues: 131 loop : -1.91 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG e 291 TYR 0.015 0.001 TYR e 100 PHE 0.023 0.002 PHE E 152 TRP 0.010 0.001 TRP D 218 HIS 0.007 0.001 HIS d 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (11711) covalent geometry : angle 0.69147 / 0.36 (16000) hydrogen bonds : bond 0.03677 / 4.02 ( 580) hydrogen bonds : angle 4.44165 / 5.31 ( 1676) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.7825 (tt0) cc_final: 0.7535 (tt0) REVERT: A 40 GLN cc_start: 0.8648 (tp40) cc_final: 0.8336 (tp-100) REVERT: D 169 GLU cc_start: 0.9290 (OUTLIER) cc_final: 0.8745 (pp20) REVERT: D 202 LEU cc_start: 0.9704 (OUTLIER) cc_final: 0.9298 (tp) REVERT: E 63 MET cc_start: 0.8656 (ptm) cc_final: 0.8334 (tmm) REVERT: E 124 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8533 (mtt) REVERT: E 192 HIS cc_start: 0.8541 (p90) cc_final: 0.8162 (p90) REVERT: E 263 MET cc_start: 0.9007 (pmm) cc_final: 0.8673 (pmm) REVERT: a 20 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7788 (tt0) REVERT: a 43 SER cc_start: 0.9538 (OUTLIER) cc_final: 0.9277 (p) REVERT: e 30 HIS cc_start: 0.7977 (OUTLIER) cc_final: 0.6945 (m170) REVERT: e 61 MET cc_start: 0.8897 (ttm) cc_final: 0.8611 (ttm) REVERT: e 63 MET cc_start: 0.9218 (ppp) cc_final: 0.9002 (ppp) REVERT: e 106 ARG cc_start: 0.9208 (mmt90) cc_final: 0.8777 (mmt-90) REVERT: e 171 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8571 (p) REVERT: e 178 LYS cc_start: 0.8368 (pttt) cc_final: 0.8011 (pttt) outliers start: 35 outliers final: 22 residues processed: 128 average time/residue: 0.1001 time to fit residues: 18.8993 Evaluate side-chains 124 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 36 ASN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain a residue 43 SER Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 81 MET Chi-restraints excluded: chain d residue 140 VAL Chi-restraints excluded: chain d residue 192 HIS Chi-restraints excluded: chain d residue 233 THR Chi-restraints excluded: chain d residue 248 THR Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 30 HIS Chi-restraints excluded: chain e residue 34 ASP Chi-restraints excluded: chain e residue 99 LYS Chi-restraints excluded: chain e residue 171 THR Chi-restraints excluded: chain e residue 180 TYR Chi-restraints excluded: chain e residue 256 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 2 optimal weight: 30.0000 chunk 121 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 43 optimal weight: 0.0980 chunk 116 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 131 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 168 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 = 0.3133 r_free = 0.3133 target = 0.043469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.032755 restraints weight = 156252.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.034406 restraints weight = 62329.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.035509 restraints weight = 36180.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.036267 restraints weight = 25254.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.036761 restraints weight = 19733.018| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11711 Z= 0.151 Angle : 0.690 12.305 16000 Z= 0.362 Chirality : 0.045 0.258 1782 Planarity : 0.004 0.043 1878 Dihedral : 18.607 83.333 1920 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.47 % Favored : 94.46 % Rotamer: Outliers : 3.27 % Allowed : 29.83 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.23), residues: 1321 helix: 0.83 (0.20), residues: 695 sheet: -1.69 (0.46), residues: 136 loop : -1.83 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG e 270 TYR 0.015 0.001 TYR D 100 PHE 0.023 0.002 PHE e 172 TRP 0.010 0.002 TRP D 73 HIS 0.006 0.001 HIS d 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (11711) covalent geometry : angle 0.68999 / 0.36 (16000) hydrogen bonds : bond 0.03599 / 3.93 ( 580) hydrogen bonds : angle 4.39042 / 5.23 ( 1676) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 95 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.7824 (tt0) cc_final: 0.7546 (tt0) REVERT: A 40 GLN cc_start: 0.8621 (tp40) cc_final: 0.8359 (tp-100) REVERT: D 169 GLU cc_start: 0.9266 (OUTLIER) cc_final: 0.8719 (pp20) REVERT: D 202 LEU cc_start: 0.9705 (OUTLIER) cc_final: 0.9304 (tp) REVERT: E 63 MET cc_start: 0.8648 (ptm) cc_final: 0.8318 (tmm) REVERT: E 124 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8548 (mtt) REVERT: E 200 LYS cc_start: 0.9463 (OUTLIER) cc_final: 0.9259 (ptpp) REVERT: a 20 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7783 (tt0) REVERT: a 43 SER cc_start: 0.9527 (OUTLIER) cc_final: 0.9264 (p) REVERT: e 30 HIS cc_start: 0.7997 (OUTLIER) cc_final: 0.7068 (m170) REVERT: e 61 MET cc_start: 0.8957 (ttm) cc_final: 0.8694 (ttm) REVERT: e 63 MET cc_start: 0.9220 (ppp) cc_final: 0.9010 (ppp) REVERT: e 106 ARG cc_start: 0.9237 (mmt90) cc_final: 0.8684 (mmt90) REVERT: e 178 LYS cc_start: 0.8403 (pttt) cc_final: 0.8053 (pttt) outliers start: 36 outliers final: 23 residues processed: 124 average time/residue: 0.1002 time to fit residues: 18.1500 Evaluate side-chains 123 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 200 LYS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain a residue 43 SER Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 101 MET Chi-restraints excluded: chain d residue 140 VAL Chi-restraints excluded: chain d residue 192 HIS Chi-restraints excluded: chain d residue 233 THR Chi-restraints excluded: chain d residue 248 THR Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 30 HIS Chi-restraints excluded: chain e residue 34 ASP Chi-restraints excluded: chain e residue 57 THR Chi-restraints excluded: chain e residue 99 LYS Chi-restraints excluded: chain e residue 180 TYR Chi-restraints excluded: chain e residue 192 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 105 optimal weight: 4.9990 chunk 2 optimal weight: 30.0000 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 44 ASN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 HIS ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 168 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 = 0.3123 r_free = 0.3123 target = 0.043067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.033149 restraints weight = 116639.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.034620 restraints weight = 52459.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.035599 restraints weight = 31883.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.036255 restraints weight = 22835.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.036727 restraints weight = 18196.023| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11711 Z= 0.150 Angle : 0.686 12.613 16000 Z= 0.359 Chirality : 0.045 0.203 1782 Planarity : 0.004 0.044 1878 Dihedral : 18.509 83.550 1918 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.62 % Favored : 94.31 % Rotamer: Outliers : 3.35 % Allowed : 29.92 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.23), residues: 1321 helix: 0.95 (0.20), residues: 697 sheet: -1.65 (0.46), residues: 136 loop : -1.80 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG a 4 TYR 0.019 0.001 TYR D 100 PHE 0.021 0.002 PHE E 152 TRP 0.009 0.002 TRP D 73 HIS 0.006 0.001 HIS d 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (11711) covalent geometry : angle 0.68571 / 0.36 (16000) hydrogen bonds : bond 0.03565 / 3.88 ( 580) hydrogen bonds : angle 4.34804 / 5.20 ( 1676) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 97 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7796 (tp30) cc_final: 0.7396 (tm-30) REVERT: A 34 GLU cc_start: 0.7864 (tt0) cc_final: 0.7601 (tt0) REVERT: A 40 GLN cc_start: 0.8679 (tp40) cc_final: 0.8425 (tp-100) REVERT: D 44 ASN cc_start: 0.9045 (OUTLIER) cc_final: 0.8660 (t0) REVERT: D 169 GLU cc_start: 0.9272 (OUTLIER) cc_final: 0.8720 (pp20) REVERT: D 202 LEU cc_start: 0.9705 (OUTLIER) cc_final: 0.9300 (tp) REVERT: E 63 MET cc_start: 0.8661 (ptm) cc_final: 0.8301 (tmm) REVERT: E 124 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8568 (mtt) REVERT: a 20 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7827 (tt0) REVERT: a 43 SER cc_start: 0.9546 (OUTLIER) cc_final: 0.9310 (p) REVERT: a 75 MET cc_start: 0.7723 (tmm) cc_final: 0.7254 (tmm) REVERT: e 30 HIS cc_start: 0.8014 (OUTLIER) cc_final: 0.7076 (m170) REVERT: e 61 MET cc_start: 0.8978 (ttm) cc_final: 0.8720 (ttm) REVERT: e 63 MET cc_start: 0.9235 (ppp) cc_final: 0.9029 (ppp) REVERT: e 106 ARG cc_start: 0.9285 (mmt90) cc_final: 0.8857 (mmt90) REVERT: e 178 LYS cc_start: 0.8390 (pttt) cc_final: 0.8048 (pttt) REVERT: e 263 MET cc_start: 0.8881 (tmm) cc_final: 0.8281 (tmm) outliers start: 37 outliers final: 23 residues processed: 126 average time/residue: 0.0955 time to fit residues: 17.4655 Evaluate side-chains 124 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 44 ASN Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain a residue 43 SER Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 101 MET Chi-restraints excluded: chain d residue 140 VAL Chi-restraints excluded: chain d residue 192 HIS Chi-restraints excluded: chain d residue 233 THR Chi-restraints excluded: chain d residue 248 THR Chi-restraints excluded: chain d residue 267 GLU Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 30 HIS Chi-restraints excluded: chain e residue 34 ASP Chi-restraints excluded: chain e residue 57 THR Chi-restraints excluded: chain e residue 99 LYS Chi-restraints excluded: chain e residue 180 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 114 optimal weight: 20.0000 chunk 37 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 168 HIS ** e 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 168 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 = 0.3103 r_free = 0.3103 target = 0.042528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.032090 restraints weight = 134472.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.033619 restraints weight = 58178.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.034639 restraints weight = 35018.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.035331 restraints weight = 25001.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.035784 restraints weight = 19936.872| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11711 Z= 0.195 Angle : 0.716 11.220 16000 Z= 0.373 Chirality : 0.046 0.212 1782 Planarity : 0.004 0.042 1878 Dihedral : 18.486 84.383 1918 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.00 % Favored : 93.85 % Rotamer: Outliers : 2.65 % Allowed : 30.45 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.23), residues: 1321 helix: 1.03 (0.20), residues: 698 sheet: -1.58 (0.45), residues: 146 loop : -1.81 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d 214 TYR 0.020 0.002 TYR D 100 PHE 0.021 0.002 PHE e 172 TRP 0.011 0.002 TRP D 73 HIS 0.008 0.001 HIS d 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (11711) covalent geometry : angle 0.71566 / 0.37 (16000) hydrogen bonds : bond 0.03667 / 4.00 ( 580) hydrogen bonds : angle 4.37714 / 5.21 ( 1676) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7843 (tp30) cc_final: 0.7465 (tm-30) REVERT: A 34 GLU cc_start: 0.8012 (tt0) cc_final: 0.7723 (tt0) REVERT: A 40 GLN cc_start: 0.8695 (tp40) cc_final: 0.8426 (tp-100) REVERT: D 202 LEU cc_start: 0.9717 (OUTLIER) cc_final: 0.9313 (tp) REVERT: E 124 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8636 (mtt) REVERT: a 20 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7894 (tt0) REVERT: a 43 SER cc_start: 0.9549 (OUTLIER) cc_final: 0.9338 (p) REVERT: e 30 HIS cc_start: 0.8186 (OUTLIER) cc_final: 0.7171 (m170) REVERT: e 61 MET cc_start: 0.9033 (ttm) cc_final: 0.8762 (ttm) REVERT: e 63 MET cc_start: 0.9312 (ppp) cc_final: 0.9109 (ppp) REVERT: e 106 ARG cc_start: 0.9338 (mmt90) cc_final: 0.8887 (mmt90) REVERT: e 178 LYS cc_start: 0.8417 (pttt) cc_final: 0.8081 (pttt) REVERT: e 263 MET cc_start: 0.8894 (tmm) cc_final: 0.8329 (tmm) REVERT: e 270 ARG cc_start: 0.9387 (tpp80) cc_final: 0.9166 (ttm110) outliers start: 29 outliers final: 21 residues processed: 116 average time/residue: 0.0969 time to fit residues: 16.7431 Evaluate side-chains 117 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain a residue 43 SER Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 101 MET Chi-restraints excluded: chain d residue 140 VAL Chi-restraints excluded: chain d residue 192 HIS Chi-restraints excluded: chain d residue 248 THR Chi-restraints excluded: chain d residue 267 GLU Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 30 HIS Chi-restraints excluded: chain e residue 34 ASP Chi-restraints excluded: chain e residue 57 THR Chi-restraints excluded: chain e residue 99 LYS Chi-restraints excluded: chain e residue 180 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 115 optimal weight: 0.1980 chunk 122 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 42 optimal weight: 0.0970 chunk 117 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 44 ASN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 168 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 = 0.3126 r_free = 0.3126 target = 0.043160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.033025 restraints weight = 140955.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.034566 restraints weight = 58643.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.035623 restraints weight = 34468.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.036318 restraints weight = 24162.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.036808 restraints weight = 18993.987| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11711 Z= 0.136 Angle : 0.693 11.896 16000 Z= 0.358 Chirality : 0.045 0.221 1782 Planarity : 0.004 0.045 1878 Dihedral : 18.387 84.496 1917 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.39 % Favored : 94.53 % Rotamer: Outliers : 2.38 % Allowed : 30.89 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.23), residues: 1321 helix: 1.08 (0.20), residues: 697 sheet: -1.47 (0.47), residues: 131 loop : -1.75 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG d 214 TYR 0.020 0.002 TYR e 100 PHE 0.023 0.002 PHE e 172 TRP 0.008 0.001 TRP E 104 HIS 0.006 0.001 HIS d 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (11711) covalent geometry : angle 0.69339 / 0.36 (16000) hydrogen bonds : bond 0.03480 / 3.81 ( 580) hydrogen bonds : angle 4.29287 / 5.09 ( 1676) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1828.01 seconds wall clock time: 32 minutes 36.87 seconds (1956.87 seconds total)