Starting phenix.real_space_refine on Wed Aug 5 20:14:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k21_36824/08_2026/8k21_36824.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k21_36824/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8k21_36824/08_2026/8k21_36824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k21_36824/08_2026/8k21_36824.map" model { file = "/net/cci-nas-00/data/ceres_data/8k21_36824/08_2026/8k21_36824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k21_36824/08_2026/8k21_36824.cif" } 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-2.2rc3-6140/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: 3.04, per 1000 atoms: 0.27 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: 0.90 Conformation dependent library (CDL) restraints added in 517.5 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: 1.01 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: 1.48 Time building geometry restraints manager: 1.20 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.660 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.140 ------------------------------------------------------------------------------- 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 : 1.303 14.150 16000 Z= 0.825 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 1.30297 / 0.82 (16000) hydrogen bonds : bond 0.17037 / 18.41 ( 580) hydrogen bonds : angle 7.33930 / 8.72 ( 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 : 0.262 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: 0.8296 (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: 0.1132 time to fit residues: 48.9466 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 : 0.386 ------------------------------------------------------------------------------- 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 4 GLN D 142 ASN D 150 ASN B D 168 HIS ** D 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 d 199 ASN e 27 GLN e 287 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.046028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.035182 restraints weight = 133735.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.036857 restraints weight = 56769.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.038006 restraints weight = 33465.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.038762 restraints weight = 23457.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.039286 restraints weight = 18427.021| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 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 = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 11711 Z= 0.180 Angle : 0.826 11.539 16000 Z= 0.442 Chirality : 0.049 0.243 1782 Planarity : 0.005 0.059 1878 Dihedral : 19.285 89.437 1951 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.39 % Favored : 94.53 % Rotamer: Outliers : 4.77 % Allowed : 33.72 % 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: -2.12 (0.21), residues: 1321 helix: -0.55 (0.18), residues: 686 sheet: -1.48 (0.51), residues: 104 loop : -2.49 (0.23), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG d 18 TYR 0.025 0.002 TYR d 284 PHE 0.023 0.002 PHE D 47 TRP 0.018 0.002 TRP e 218 HIS 0.014 0.002 HIS e 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (11711) covalent geometry : angle 0.82577 / 0.44 (16000) hydrogen bonds : bond 0.04812 / 5.30 ( 580) hydrogen bonds : angle 5.20192 / 6.19 ( 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 202 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 149 time to evaluate : 0.390 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: 0.7939 (tt0) cc_final: 0.7448 (tt0) REVERT: A 40 GLN cc_start: 0.8374 (tp40) cc_final: 0.8085 (tp-100) REVERT: D 101 MET cc_start: 0.8455 (mmt) cc_final: 0.8172 (tpt) REVERT: D 202 LEU cc_start: 0.9694 (OUTLIER) cc_final: 0.9297 (tp) REVERT: e 61 MET cc_start: 0.8826 (ttm) cc_final: 0.8424 (ttm) REVERT: e 288 ASN cc_start: 0.9199 (m-40) cc_final: 0.8964 (m110) outliers start: 53 outliers final: 23 residues processed: 185 average time/residue: 0.0914 time to fit residues: 24.4358 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 : 0.250 ------------------------------------------------------------------------------- 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 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 40 VAL 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 73 VAL Chi-restraints excluded: chain d residue 39 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 126 VAL Chi-restraints excluded: chain e residue 183 GLU Chi-restraints excluded: chain e residue 192 HIS 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: 10.0000 chunk 115 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 77 optimal weight: 0.0980 chunk 121 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 ASN D 158 GLN D 192 HIS ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 ASN a 72 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.044441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.033727 restraints weight = 153181.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.035439 restraints weight = 59290.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.036606 restraints weight = 33685.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.037381 restraints weight = 22986.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.037931 restraints weight = 17639.284| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11711 Z= 0.172 Angle : 0.739 13.959 16000 Z= 0.393 Chirality : 0.046 0.205 1782 Planarity : 0.005 0.055 1878 Dihedral : 18.980 83.090 1922 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.39 % Favored : 94.53 % Rotamer: Outliers : 4.15 % Allowed : 31.95 % Favored : 63.90 % 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: -1.49 (0.22), residues: 1321 helix: 0.09 (0.19), residues: 686 sheet: -1.58 (0.47), residues: 112 loop : -2.30 (0.24), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG e 144 TYR 0.017 0.002 TYR d 284 PHE 0.028 0.002 PHE E 276 TRP 0.009 0.002 TRP D 218 HIS 0.011 0.001 HIS D 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (11711) covalent geometry : angle 0.73864 / 0.39 (16000) hydrogen bonds : bond 0.04175 / 4.68 ( 580) hydrogen bonds : angle 4.83329 / 5.76 ( 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 166 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 120 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8035 (tt0) cc_final: 0.7737 (tt0) REVERT: A 40 GLN cc_start: 0.8418 (tp40) cc_final: 0.8144 (tp-100) REVERT: D 61 MET cc_start: 0.9537 (mmm) cc_final: 0.9310 (mmm) REVERT: D 124 MET cc_start: 0.8754 (mtp) cc_final: 0.8219 (ptp) REVERT: D 169 GLU cc_start: 0.9411 (OUTLIER) cc_final: 0.8948 (pp20) REVERT: D 202 LEU cc_start: 0.9707 (OUTLIER) cc_final: 0.9316 (tp) REVERT: a 20 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8080 (mp0) REVERT: e 10 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8222 (pttm) REVERT: e 30 HIS cc_start: 0.7903 (OUTLIER) cc_final: 0.6986 (m170) REVERT: e 61 MET cc_start: 0.8778 (ttm) cc_final: 0.8382 (ttm) REVERT: e 125 ARG cc_start: 0.9205 (tpp80) cc_final: 0.8932 (tpp80) REVERT: e 178 LYS cc_start: 0.8443 (pttt) cc_final: 0.8189 (pttt) outliers start: 46 outliers final: 24 residues processed: 149 average time/residue: 0.0947 time to fit residues: 20.4001 Evaluate side-chains 133 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 E residue 40 VAL Chi-restraints excluded: chain E residue 124 MET 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 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 133 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 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 81 MET Chi-restraints excluded: chain e residue 192 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 1 optimal weight: 30.0000 chunk 7 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 53 optimal weight: 0.1980 chunk 14 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 36 HIS ** a 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 72 ASN d 150 ASN B ** d 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 = 0.3153 r_free = 0.3153 target = 0.044132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.033758 restraints weight = 143527.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.035392 restraints weight = 59194.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.036485 restraints weight = 34593.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.037237 restraints weight = 24057.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.037704 restraints weight = 18714.885| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 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 = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11711 Z= 0.176 Angle : 0.711 12.215 16000 Z= 0.379 Chirality : 0.045 0.177 1782 Planarity : 0.004 0.045 1878 Dihedral : 18.916 83.852 1922 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.24 % Favored : 94.68 % Rotamer: Outliers : 3.97 % Allowed : 29.66 % Favored : 66.37 % 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: -1.18 (0.23), residues: 1321 helix: 0.40 (0.20), residues: 688 sheet: -1.89 (0.42), residues: 146 loop : -2.09 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG e 106 TYR 0.019 0.001 TYR d 284 PHE 0.026 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 0.00386 / 0.18 (11711) covalent geometry : angle 0.71113 / 0.38 (16000) hydrogen bonds : bond 0.04016 / 4.46 ( 580) hydrogen bonds : angle 4.69201 / 5.61 ( 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 149 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 105 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.7900 (tt0) cc_final: 0.7631 (tt0) REVERT: A 54 LYS cc_start: 0.8886 (ttmt) cc_final: 0.8594 (ttmt) REVERT: D 124 MET cc_start: 0.8733 (mtp) cc_final: 0.8477 (ptp) REVERT: D 169 GLU cc_start: 0.9341 (OUTLIER) cc_final: 0.8865 (pp20) REVERT: D 202 LEU cc_start: 0.9706 (OUTLIER) cc_final: 0.9292 (tp) REVERT: D 294 MET cc_start: 0.7771 (ppp) cc_final: 0.7539 (ppp) REVERT: E 63 MET cc_start: 0.8668 (ptm) cc_final: 0.8333 (tmm) REVERT: E 192 HIS cc_start: 0.8442 (p90) cc_final: 0.8111 (p90) REVERT: a 20 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8007 (mt-10) REVERT: a 43 SER cc_start: 0.9493 (OUTLIER) cc_final: 0.9243 (p) REVERT: e 30 HIS cc_start: 0.7991 (OUTLIER) cc_final: 0.7065 (m170) REVERT: e 61 MET cc_start: 0.8835 (ttm) cc_final: 0.8550 (ttm) REVERT: e 178 LYS cc_start: 0.8400 (pttt) cc_final: 0.8120 (pttt) REVERT: e 288 ASN cc_start: 0.9263 (m-40) cc_final: 0.9002 (m110) outliers start: 44 outliers final: 24 residues processed: 138 average time/residue: 0.0799 time to fit residues: 16.6659 Evaluate side-chains 128 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 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 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 25 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 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 81 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 115 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 84 optimal weight: 0.0970 chunk 109 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 158 GLN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN E 58 ASN a 40 GLN ** d 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.044470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.033735 restraints weight = 171401.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.035444 restraints weight = 64652.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.036641 restraints weight = 36471.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.037431 restraints weight = 24804.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.038005 restraints weight = 19002.401| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11711 Z= 0.137 Angle : 0.669 11.336 16000 Z= 0.354 Chirality : 0.044 0.164 1782 Planarity : 0.004 0.046 1878 Dihedral : 18.808 83.668 1922 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.16 % Favored : 94.76 % Rotamer: Outliers : 3.80 % Allowed : 29.39 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.23), residues: 1321 helix: 0.55 (0.20), residues: 692 sheet: -1.83 (0.45), residues: 131 loop : -1.89 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG e 106 TYR 0.019 0.001 TYR a 62 PHE 0.022 0.002 PHE A 68 TRP 0.011 0.001 TRP D 218 HIS 0.008 0.001 HIS d 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (11711) covalent geometry : angle 0.66947 / 0.35 (16000) hydrogen bonds : bond 0.03683 / 4.08 ( 580) hydrogen bonds : angle 4.48120 / 5.34 ( 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 154 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 112 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.9793 (mt) cc_final: 0.9543 (tp) REVERT: A 34 GLU cc_start: 0.7821 (tt0) cc_final: 0.7543 (tt0) REVERT: D 124 MET cc_start: 0.8862 (mtp) cc_final: 0.8661 (ptp) REVERT: D 169 GLU cc_start: 0.9322 (OUTLIER) cc_final: 0.8847 (pp20) REVERT: D 202 LEU cc_start: 0.9689 (OUTLIER) cc_final: 0.9282 (tp) REVERT: D 294 MET cc_start: 0.7790 (ppp) cc_final: 0.7542 (ppp) REVERT: E 1 MET cc_start: 0.8036 (tpp) cc_final: 0.7758 (tpt) REVERT: E 63 MET cc_start: 0.8587 (ptm) cc_final: 0.8244 (tmm) REVERT: E 124 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8409 (mtt) REVERT: E 192 HIS cc_start: 0.8419 (p90) cc_final: 0.8068 (p90) REVERT: E 263 MET cc_start: 0.8768 (pmm) cc_final: 0.8527 (pmm) REVERT: a 43 SER cc_start: 0.9484 (OUTLIER) cc_final: 0.9245 (p) REVERT: e 30 HIS cc_start: 0.7974 (OUTLIER) cc_final: 0.7110 (m170) REVERT: e 61 MET cc_start: 0.8834 (ttm) cc_final: 0.8555 (ttm) REVERT: e 106 ARG cc_start: 0.9125 (mmt90) cc_final: 0.8529 (mmt90) REVERT: e 178 LYS cc_start: 0.8394 (pttt) cc_final: 0.8117 (pttt) outliers start: 42 outliers final: 20 residues processed: 143 average time/residue: 0.0888 time to fit residues: 18.7513 Evaluate side-chains 125 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 158 GLN 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 81 MET Chi-restraints excluded: chain d residue 133 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 57 THR Chi-restraints excluded: chain e residue 81 MET Chi-restraints excluded: chain e residue 256 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 63 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 17 optimal weight: 0.0060 chunk 112 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 158 GLN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 134 HIS ** d 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.044446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.034292 restraints weight = 119918.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.035822 restraints weight = 53903.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.036874 restraints weight = 32640.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.037590 restraints weight = 23218.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.038063 restraints weight = 18314.198| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11711 Z= 0.140 Angle : 0.672 11.323 16000 Z= 0.357 Chirality : 0.045 0.214 1782 Planarity : 0.004 0.046 1878 Dihedral : 18.707 83.223 1920 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.39 % Favored : 94.53 % Rotamer: Outliers : 3.09 % Allowed : 30.45 % 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: -0.87 (0.23), residues: 1321 helix: 0.63 (0.20), residues: 694 sheet: -1.80 (0.45), residues: 131 loop : -1.95 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG e 291 TYR 0.016 0.001 TYR a 62 PHE 0.032 0.002 PHE A 68 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 0.00312 / 0.14 (11711) covalent geometry : angle 0.67172 / 0.36 (16000) hydrogen bonds : bond 0.03721 / 4.13 ( 580) hydrogen bonds : angle 4.45682 / 5.34 ( 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 139 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.9788 (mt) cc_final: 0.9520 (tp) REVERT: A 34 GLU cc_start: 0.7813 (tt0) cc_final: 0.7491 (tt0) REVERT: D 61 MET cc_start: 0.9472 (mmm) cc_final: 0.9251 (mmm) REVERT: D 169 GLU cc_start: 0.9325 (OUTLIER) cc_final: 0.8852 (pp20) REVERT: D 202 LEU cc_start: 0.9683 (OUTLIER) cc_final: 0.9282 (tp) REVERT: D 294 MET cc_start: 0.7787 (ppp) cc_final: 0.7543 (ppp) REVERT: E 1 MET cc_start: 0.7973 (tpp) cc_final: 0.7705 (tpt) REVERT: E 124 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8452 (mtt) REVERT: E 192 HIS cc_start: 0.8396 (p90) cc_final: 0.8032 (p90) REVERT: a 43 SER cc_start: 0.9519 (OUTLIER) cc_final: 0.9282 (p) REVERT: e 30 HIS cc_start: 0.8072 (OUTLIER) cc_final: 0.7142 (m170) REVERT: e 61 MET cc_start: 0.8862 (ttm) cc_final: 0.8556 (ttm) REVERT: e 106 ARG cc_start: 0.9186 (mmt90) cc_final: 0.8513 (mmt90) REVERT: e 178 LYS cc_start: 0.8362 (pttt) cc_final: 0.8010 (pttt) outliers start: 34 outliers final: 20 residues processed: 132 average time/residue: 0.1074 time to fit residues: 20.7637 Evaluate side-chains 124 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 57 THR Chi-restraints excluded: chain e residue 81 MET Chi-restraints excluded: chain e residue 99 LYS 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: 0.8980 chunk 41 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 chunk 118 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN d 89 HIS ** d 168 HIS ** 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 = 0.3157 r_free = 0.3157 target = 0.044304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.033709 restraints weight = 167228.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.035394 restraints weight = 63920.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.036570 restraints weight = 36251.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.037354 restraints weight = 24711.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.037837 restraints weight = 18946.282| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11711 Z= 0.141 Angle : 0.668 11.465 16000 Z= 0.355 Chirality : 0.045 0.188 1782 Planarity : 0.004 0.046 1878 Dihedral : 18.613 82.812 1920 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.39 % Favored : 94.53 % Rotamer: Outliers : 3.18 % Allowed : 30.54 % Favored : 66.28 % 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: -0.81 (0.23), residues: 1321 helix: 0.67 (0.20), residues: 693 sheet: -1.63 (0.45), residues: 141 loop : -1.93 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG e 291 TYR 0.015 0.001 TYR a 62 PHE 0.033 0.002 PHE A 68 TRP 0.009 0.001 TRP D 218 HIS 0.007 0.001 HIS d 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (11711) covalent geometry : angle 0.66776 / 0.35 (16000) hydrogen bonds : bond 0.03646 / 4.03 ( 580) hydrogen bonds : angle 4.40220 / 5.26 ( 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 141 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 0.454 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: 0.9775 (mt) cc_final: 0.9514 (tp) REVERT: A 34 GLU cc_start: 0.7781 (tt0) cc_final: 0.7462 (tt0) REVERT: D 61 MET cc_start: 0.9461 (mmm) cc_final: 0.9225 (mmm) REVERT: D 169 GLU cc_start: 0.9310 (OUTLIER) cc_final: 0.8830 (pp20) REVERT: D 202 LEU cc_start: 0.9690 (OUTLIER) cc_final: 0.9291 (tp) REVERT: D 294 MET cc_start: 0.7759 (ppp) cc_final: 0.7535 (ppp) REVERT: E 1 MET cc_start: 0.7972 (tpp) cc_final: 0.7667 (tpt) REVERT: E 63 MET cc_start: 0.8566 (ptm) cc_final: 0.8352 (ppp) REVERT: E 124 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8548 (mtt) REVERT: E 192 HIS cc_start: 0.8393 (p90) cc_final: 0.8040 (p90) REVERT: a 43 SER cc_start: 0.9524 (OUTLIER) cc_final: 0.9268 (p) REVERT: e 30 HIS cc_start: 0.8047 (OUTLIER) cc_final: 0.7115 (m170) REVERT: e 61 MET cc_start: 0.8910 (ttm) cc_final: 0.8707 (ttm) REVERT: e 63 MET cc_start: 0.9166 (ppp) cc_final: 0.8952 (ppp) REVERT: e 106 ARG cc_start: 0.9210 (mmt90) cc_final: 0.8499 (mmt90) REVERT: e 178 LYS cc_start: 0.8324 (pttt) cc_final: 0.7983 (pttt) outliers start: 35 outliers final: 21 residues processed: 133 average time/residue: 0.1112 time to fit residues: 21.7348 Evaluate side-chains 128 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 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 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 233 THR Chi-restraints excluded: chain d residue 244 ASP 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 99 LYS 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: 2.9990 chunk 86 optimal weight: 8.9990 chunk 69 optimal weight: 0.4980 chunk 43 optimal weight: 10.0000 chunk 116 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 81 optimal weight: 0.3980 chunk 32 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 287 ASN B ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN ** d 168 HIS ** 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 = 0.3165 r_free = 0.3165 target = 0.044547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.034063 restraints weight = 155556.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.035744 restraints weight = 60678.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.036899 restraints weight = 34695.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.037672 restraints weight = 23717.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.038179 restraints weight = 18245.127| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11711 Z= 0.136 Angle : 0.667 11.291 16000 Z= 0.355 Chirality : 0.045 0.187 1782 Planarity : 0.004 0.047 1878 Dihedral : 18.502 82.218 1920 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.24 % Favored : 94.68 % Rotamer: Outliers : 3.09 % Allowed : 30.36 % Favored : 66.55 % 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: -0.76 (0.23), residues: 1321 helix: 0.71 (0.20), residues: 695 sheet: -1.67 (0.47), residues: 131 loop : -1.90 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG e 291 TYR 0.016 0.001 TYR e 100 PHE 0.041 0.002 PHE A 68 TRP 0.009 0.001 TRP D 218 HIS 0.006 0.001 HIS d 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (11711) covalent geometry : angle 0.66698 / 0.35 (16000) hydrogen bonds : bond 0.03565 / 3.93 ( 580) hydrogen bonds : angle 4.33762 / 5.16 ( 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 139 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.456 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: 0.9784 (mt) cc_final: 0.9537 (tp) REVERT: A 34 GLU cc_start: 0.7784 (tt0) cc_final: 0.7357 (tt0) REVERT: D 61 MET cc_start: 0.9487 (mmm) cc_final: 0.9241 (mmm) REVERT: D 169 GLU cc_start: 0.9323 (OUTLIER) cc_final: 0.8844 (pp20) REVERT: D 202 LEU cc_start: 0.9687 (OUTLIER) cc_final: 0.9296 (tp) REVERT: D 294 MET cc_start: 0.7770 (ppp) cc_final: 0.7537 (ppp) REVERT: E 1 MET cc_start: 0.7919 (tpp) cc_final: 0.7696 (tpt) REVERT: E 61 MET cc_start: 0.8920 (mmm) cc_final: 0.8633 (mpp) REVERT: E 63 MET cc_start: 0.8614 (ptm) cc_final: 0.8343 (ppp) REVERT: E 124 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8554 (mtt) REVERT: E 192 HIS cc_start: 0.8487 (p90) cc_final: 0.8153 (p90) REVERT: E 214 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8590 (ptp-110) REVERT: a 43 SER cc_start: 0.9491 (OUTLIER) cc_final: 0.9245 (p) REVERT: e 30 HIS cc_start: 0.7902 (OUTLIER) cc_final: 0.6972 (m170) REVERT: e 61 MET cc_start: 0.8921 (ttm) cc_final: 0.8623 (ttm) REVERT: e 63 MET cc_start: 0.9188 (ppp) cc_final: 0.8979 (ppp) REVERT: e 106 ARG cc_start: 0.9314 (mmt90) cc_final: 0.8978 (mmt-90) REVERT: e 178 LYS cc_start: 0.8330 (pttt) cc_final: 0.7988 (pttt) outliers start: 34 outliers final: 21 residues processed: 133 average time/residue: 0.1126 time to fit residues: 21.7678 Evaluate side-chains 125 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 214 ARG Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain a residue 5 ILE 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 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 57 THR Chi-restraints excluded: chain e residue 99 LYS Chi-restraints excluded: chain e residue 180 TYR Chi-restraints excluded: chain e residue 256 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 105 optimal weight: 0.7980 chunk 2 optimal weight: 30.0000 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 11 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 131 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 168 HIS ** 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 158 GLN ** 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 = 0.3161 r_free = 0.3161 target = 0.044251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.034305 restraints weight = 116269.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.035798 restraints weight = 52553.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.036824 restraints weight = 31884.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.037522 restraints weight = 22610.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.037985 restraints weight = 17826.110| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11711 Z= 0.147 Angle : 0.688 10.970 16000 Z= 0.364 Chirality : 0.045 0.200 1782 Planarity : 0.004 0.046 1878 Dihedral : 18.445 81.743 1918 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.09 % Favored : 94.84 % Rotamer: Outliers : 2.82 % Allowed : 30.89 % Favored : 66.28 % 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: -0.66 (0.23), residues: 1321 helix: 0.78 (0.20), residues: 696 sheet: -1.62 (0.47), residues: 131 loop : -1.86 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG e 291 TYR 0.016 0.001 TYR d 275 PHE 0.053 0.002 PHE A 68 TRP 0.009 0.001 TRP D 218 HIS 0.007 0.001 HIS d 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (11711) covalent geometry : angle 0.68767 / 0.36 (16000) hydrogen bonds : bond 0.03608 / 3.99 ( 580) hydrogen bonds : angle 4.33178 / 5.16 ( 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 131 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.9782 (mt) cc_final: 0.9539 (tp) REVERT: A 34 GLU cc_start: 0.7632 (tt0) cc_final: 0.7216 (tt0) REVERT: A 68 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.8102 (m-10) REVERT: D 61 MET cc_start: 0.9480 (mmm) cc_final: 0.9242 (mmm) REVERT: D 169 GLU cc_start: 0.9298 (OUTLIER) cc_final: 0.8820 (pp20) REVERT: D 202 LEU cc_start: 0.9688 (OUTLIER) cc_final: 0.9296 (tp) REVERT: D 294 MET cc_start: 0.7753 (ppp) cc_final: 0.7538 (ppp) REVERT: E 61 MET cc_start: 0.8998 (mmm) cc_final: 0.8765 (mmm) REVERT: E 63 MET cc_start: 0.8607 (ptm) cc_final: 0.8244 (tmm) REVERT: E 124 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8557 (mtt) REVERT: E 192 HIS cc_start: 0.8476 (p90) cc_final: 0.8131 (p90) REVERT: E 214 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8594 (ptp-110) REVERT: a 43 SER cc_start: 0.9511 (OUTLIER) cc_final: 0.9256 (p) REVERT: e 30 HIS cc_start: 0.7769 (OUTLIER) cc_final: 0.6853 (m170) REVERT: e 61 MET cc_start: 0.8906 (ttm) cc_final: 0.8612 (ttm) REVERT: e 63 MET cc_start: 0.9174 (ppp) cc_final: 0.8969 (ppp) REVERT: e 106 ARG cc_start: 0.9287 (mmt90) cc_final: 0.8810 (mmt90) REVERT: e 178 LYS cc_start: 0.8365 (pttt) cc_final: 0.8025 (pttt) outliers start: 31 outliers final: 19 residues processed: 126 average time/residue: 0.1088 time to fit residues: 19.9279 Evaluate side-chains 121 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 169 GLU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 212 ILE 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 214 ARG 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 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 Chi-restraints excluded: chain e residue 256 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 114 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 107 optimal weight: 0.0030 chunk 101 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 106 optimal weight: 0.4980 chunk 119 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 25 ASN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 HIS ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 168 HIS ** 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 158 GLN ** 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 = 0.3175 r_free = 0.3175 target = 0.044708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.034384 restraints weight = 131858.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.035990 restraints weight = 56127.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.037078 restraints weight = 33230.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.037816 restraints weight = 23231.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.038319 restraints weight = 18148.569| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11711 Z= 0.135 Angle : 0.695 11.122 16000 Z= 0.364 Chirality : 0.046 0.246 1782 Planarity : 0.004 0.047 1878 Dihedral : 18.362 81.062 1918 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.16 % Favored : 94.76 % Rotamer: Outliers : 2.47 % Allowed : 30.71 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.23), residues: 1321 helix: 0.81 (0.20), residues: 693 sheet: -1.50 (0.48), residues: 129 loop : -1.73 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG e 291 TYR 0.018 0.001 TYR e 100 PHE 0.045 0.002 PHE A 68 TRP 0.009 0.001 TRP D 218 HIS 0.006 0.001 HIS d 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (11711) covalent geometry : angle 0.69473 / 0.36 (16000) hydrogen bonds : bond 0.03590 / 3.99 ( 580) hydrogen bonds : angle 4.30759 / 5.16 ( 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 127 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.9788 (mt) cc_final: 0.9533 (tp) REVERT: A 46 GLN cc_start: 0.9088 (tp-100) cc_final: 0.8670 (tt0) REVERT: A 68 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: D 61 MET cc_start: 0.9483 (mmm) cc_final: 0.9239 (mmm) REVERT: D 169 GLU cc_start: 0.9304 (OUTLIER) cc_final: 0.8748 (pp20) REVERT: D 202 LEU cc_start: 0.9684 (OUTLIER) cc_final: 0.9292 (tp) REVERT: D 294 MET cc_start: 0.7660 (ppp) cc_final: 0.7419 (ppp) REVERT: E 61 MET cc_start: 0.9026 (mmm) cc_final: 0.8772 (mmm) REVERT: E 124 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8569 (mtt) REVERT: E 192 HIS cc_start: 0.8544 (p90) cc_final: 0.8203 (p90) REVERT: E 214 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8595 (ptp-110) REVERT: a 43 SER cc_start: 0.9480 (OUTLIER) cc_final: 0.9219 (p) REVERT: a 75 MET cc_start: 0.7572 (tmm) cc_final: 0.7094 (tmm) REVERT: e 30 HIS cc_start: 0.7863 (OUTLIER) cc_final: 0.6923 (m170) REVERT: e 61 MET cc_start: 0.8931 (ttm) cc_final: 0.8627 (ttm) REVERT: e 106 ARG cc_start: 0.9312 (mmt90) cc_final: 0.8799 (mmt90) REVERT: e 124 MET cc_start: 0.8974 (ptp) cc_final: 0.8743 (ptt) REVERT: e 178 LYS cc_start: 0.8362 (pttt) cc_final: 0.8016 (pttt) outliers start: 27 outliers final: 17 residues processed: 120 average time/residue: 0.1119 time to fit residues: 19.5872 Evaluate side-chains 119 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 169 GLU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 212 ILE 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 214 ARG 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 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 57 THR Chi-restraints excluded: chain e residue 99 LYS Chi-restraints excluded: chain e residue 180 TYR Chi-restraints excluded: chain e residue 256 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 36 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 115 optimal weight: 0.1980 chunk 122 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 117 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 26 optimal weight: 0.0070 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 168 HIS ** 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 = 0.3182 r_free = 0.3182 target = 0.044945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.034500 restraints weight = 139113.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.036115 restraints weight = 58759.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.037240 restraints weight = 34551.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.037977 restraints weight = 24027.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.038510 restraints weight = 18674.463| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11711 Z= 0.132 Angle : 0.703 11.165 16000 Z= 0.365 Chirality : 0.047 0.329 1782 Planarity : 0.004 0.047 1878 Dihedral : 18.272 80.170 1917 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.09 % Favored : 94.84 % Rotamer: Outliers : 2.03 % Allowed : 31.69 % Favored : 66.28 % 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: -0.52 (0.23), residues: 1321 helix: 0.85 (0.20), residues: 695 sheet: -1.47 (0.48), residues: 129 loop : -1.72 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG e 291 TYR 0.018 0.001 TYR e 100 PHE 0.037 0.002 PHE A 68 TRP 0.009 0.001 TRP D 218 HIS 0.006 0.001 HIS d 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (11711) covalent geometry : angle 0.70250 / 0.37 (16000) hydrogen bonds : bond 0.03571 / 3.99 ( 580) hydrogen bonds : angle 4.30732 / 5.17 ( 1676) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1864.70 seconds wall clock time: 33 minutes 15.89 seconds (1995.89 seconds total)