Starting phenix.real_space_refine on Sat Aug 23 10:55:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k21_36824/08_2025/8k21_36824.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k21_36824/08_2025/8k21_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_2025/8k21_36824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k21_36824/08_2025/8k21_36824.map" model { file = "/net/cci-nas-00/data/ceres_data/8k21_36824/08_2025/8k21_36824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k21_36824/08_2025/8k21_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-2.0-5787/lib/python3.9/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: 3.63, per 1000 atoms: 0.32 Number of scatterers: 11389 At special positions: 0 Unit cell: (107.8, 119.9, 129.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 41 15.00 O 2190 8.00 N 1947 7.00 C 7148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 664.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.35 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: 1.94 Time building geometry restraints manager: 1.26 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: 15336 2.83 - 5.66: 525 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: 1498 0.097 - 0.194: 228 0.194 - 0.291: 42 0.291 - 0.388: 12 0.388 - 0.485: 2 Chirality restraints: 1782 Sorted by residual: chirality pdb=" CB ILE D 245 " pdb=" CA ILE D 245 " pdb=" CG1 ILE D 245 " pdb=" CG2 ILE D 245 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.88e+00 chirality pdb=" CB VAL e 105 " pdb=" CA VAL e 105 " pdb=" CG1 VAL e 105 " pdb=" CG2 VAL e 105 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" CA ILE d 251 " pdb=" N ILE d 251 " pdb=" C ILE d 251 " pdb=" CB ILE d 251 " both_signs ideal model delta sigma weight residual False 2.43 2.05 0.38 2.00e-01 2.50e+01 3.60e+00 ... (remaining 1779 not shown) Planarity restraints: 1878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 255 " -0.025 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C ALA E 255 " 0.089 2.00e-02 2.50e+03 pdb=" O ALA E 255 " -0.035 2.00e-02 2.50e+03 pdb=" N PHE E 256 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA d 209 " -0.023 2.00e-02 2.50e+03 4.68e-02 2.19e+01 pdb=" C ALA d 209 " 0.081 2.00e-02 2.50e+03 pdb=" O ALA d 209 " -0.030 2.00e-02 2.50e+03 pdb=" N TYR d 210 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 268 " 0.024 2.00e-02 2.50e+03 2.77e-02 1.35e+01 pdb=" CG PHE E 268 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 PHE E 268 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE E 268 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE E 268 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE E 268 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE E 268 " 0.003 2.00e-02 2.50e+03 ... (remaining 1875 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2126 2.77 - 3.30: 10428 3.30 - 3.83: 21040 3.83 - 4.37: 24563 4.37 - 4.90: 39521 Nonbonded interactions: 97678 Sorted by model distance: nonbonded pdb=" O THR d 171 " pdb=" OG SER d 175 " model vdw 2.232 3.040 nonbonded pdb=" O ASP e 153 " pdb=" OG1 THR e 157 " model vdw 2.251 3.040 nonbonded pdb=" OD1 ASP d 127 " pdb=" OH TYR d 284 " model vdw 2.252 3.040 nonbonded pdb=" O ASP d 153 " pdb=" OG1 THR d 157 " model vdw 2.258 3.040 nonbonded pdb=" O SER D 225 " pdb=" OG SER D 225 " model vdw 2.264 3.040 ... (remaining 97673 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 9 or (resid 10 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 14 or (resid 15 and (name \ N or name CA or name C or name O or name CB )) or resid 16 through 75)) selection = chain 'a' } ncs_group { reference = (chain 'D' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 74 or (resid 75 and (name N or name \ CA or name C or name O or name CB )) or resid 76 through 141 or (resid 142 and \ (name N or name CA or name C or name O or name CB )) or resid 143 through 149 or \ resid 151 through 234 or (resid 235 and (name N or name CA or name C or name O \ or name CB )) or resid 236 through 286 or resid 288 through 295)) selection = (chain 'E' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 74 or (resid 75 and (name N or name \ CA or name C or name O or name CB )) or resid 76 through 78 or (resid 79 throug \ h 84 and (name N or name CA or name C or name O or name CB )) or resid 85 throug \ h 110 or (resid 111 and (name N or name CA or name C or name O or name CB )) or \ resid 112 or (resid 113 and (name N or name CA or name C or name O or name CB )) \ or resid 114 through 118 or (resid 119 and (name N or name CA or name C or name \ O or name CB )) or resid 120 through 141 or (resid 142 and (name N or name CA o \ r name C or name O or name CB )) or resid 143 through 149 or resid 151 through 2 \ 34 or (resid 235 and (name N or name CA or name C or name O or name CB )) or res \ id 236 through 286 or resid 288 through 295)) selection = (chain 'd' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 74 or (resid 75 and (name N or name \ CA or name C or name O or name CB )) or resid 76 through 78 or (resid 79 throug \ h 84 and (name N or name CA or name C or name O or name CB )) or resid 85 throug \ h 110 or (resid 111 and (name N or name CA or name C or name O or name CB )) or \ resid 112 or (resid 113 and (name N or name CA or name C or name O or name CB )) \ or resid 114 through 118 or (resid 119 and (name N or name CA or name C or name \ O or name CB )) or resid 120 through 149 or resid 151 through 234 or (resid 235 \ and (name N or name CA or name C or name O or name CB )) or resid 236 through 2 \ 86 or resid 288 through 295)) selection = (chain 'e' and (resid 1 through 78 or (resid 79 through 84 and (name N or name C \ A or name C or name O or name CB )) or resid 85 through 110 or (resid 111 and (n \ ame N or name CA or name C or name O or name CB )) or resid 112 or (resid 113 an \ d (name N or name CA or name C or name O or name CB )) or resid 114 through 118 \ or (resid 119 and (name N or name CA or name C or name O or name CB )) or resid \ 120 through 141 or (resid 142 and (name N or name CA or name C or name O or name \ CB )) or resid 143 through 149 or resid 151 through 286 or resid 288 through 29 \ 5)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.15 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 13.570 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 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= 0.546 Angle : 1.288 14.150 16000 Z= 0.783 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 aren 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 covalent geometry : bond 0.00899 (11711) covalent geometry : angle 1.28761 (16000) hydrogen bonds : bond 0.17037 ( 580) hydrogen bonds : angle 7.33930 ( 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 : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.7258 (tt0) cc_final: 0.6779 (tt0) REVERT: E 260 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.8295 (m-30) REVERT: a 48 LYS cc_start: 0.8649 (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: 0.1350 time to fit residues: 57.8735 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 : 0.420 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: D 4 GLN D 142 ASN D 150 ASN B D 168 HIS D 192 HIS D 257 HIS D 279 ASN E 44 ASN E 132 HIS E 134 HIS E 261 GLN a 72 ASN d 199 ASN e 27 GLN e 132 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.045786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.034974 restraints weight = 146983.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.036665 restraints weight = 59774.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.037846 restraints weight = 34618.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.038632 restraints weight = 23938.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.039106 restraints weight = 18603.784| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 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 = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3033 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= 0.162 Angle : 0.738 10.442 16000 Z= 0.397 Chirality : 0.045 0.191 1782 Planarity : 0.005 0.055 1878 Dihedral : 18.955 83.047 1951 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.54 % Favored : 94.31 % Rotamer: Outliers : 4.41 % Allowed : 33.72 % Favored : 61.87 % 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 aren not related in a simple way. whole: -1.86 (0.21), residues: 1321 helix: -0.38 (0.18), residues: 691 sheet: -1.40 (0.47), residues: 114 loop : -2.33 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG d 18 TYR 0.022 0.002 TYR d 284 PHE 0.024 0.002 PHE e 152 TRP 0.015 0.002 TRP e 218 HIS 0.013 0.001 HIS D 192 Details of bonding type rmsd covalent geometry : bond 0.00372 (11711) covalent geometry : angle 0.73835 (16000) hydrogen bonds : bond 0.04193 ( 580) hydrogen bonds : angle 4.89283 ( 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 192 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 143 time to evaluate : 0.330 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: A 34 GLU cc_start: 0.7935 (tt0) cc_final: 0.7430 (tt0) REVERT: A 40 GLN cc_start: 0.8366 (tp40) cc_final: 0.8052 (tp-100) REVERT: D 50 LEU cc_start: 0.9307 (mt) cc_final: 0.9076 (mt) REVERT: D 101 MET cc_start: 0.8415 (mmt) cc_final: 0.8140 (tpt) REVERT: D 202 LEU cc_start: 0.9694 (OUTLIER) cc_final: 0.9316 (tp) REVERT: E 261 GLN cc_start: 0.9362 (OUTLIER) cc_final: 0.9095 (mp10) REVERT: a 20 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7830 (mp0) REVERT: a 72 ASN cc_start: 0.9049 (OUTLIER) cc_final: 0.8819 (t0) REVERT: e 6 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7897 (mm) REVERT: e 61 MET cc_start: 0.8863 (ttm) cc_final: 0.8558 (ttm) outliers start: 49 outliers final: 20 residues processed: 177 average time/residue: 0.1069 time to fit residues: 26.9496 Evaluate side-chains 144 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 46 VAL 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 126 VAL Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 261 GLN Chi-restraints excluded: chain E residue 276 PHE Chi-restraints excluded: chain a residue 43 SER Chi-restraints excluded: chain a residue 72 ASN Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain d residue 153 ASP 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 266 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 29 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 115 optimal weight: 0.4980 chunk 91 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 ASN E 25 ASN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 36 HIS a 61 ASN d 36 ASN d 134 HIS ** d 150 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** d 168 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.045271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.034494 restraints weight = 154629.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.036181 restraints weight = 61664.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.037348 restraints weight = 35668.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.038136 restraints weight = 24554.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.038664 restraints weight = 18992.906| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 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 = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11711 Z= 0.145 Angle : 0.680 12.666 16000 Z= 0.360 Chirality : 0.043 0.218 1782 Planarity : 0.004 0.052 1878 Dihedral : 18.513 84.563 1925 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.32 % Favored : 94.53 % Rotamer: Outliers : 3.80 % Allowed : 31.69 % Favored : 64.52 % 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 aren not related in a simple way. whole: -1.16 (0.23), residues: 1321 helix: 0.32 (0.19), residues: 700 sheet: -1.94 (0.43), residues: 136 loop : -1.98 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG d 18 TYR 0.015 0.001 TYR d 284 PHE 0.022 0.002 PHE E 276 TRP 0.011 0.001 TRP D 218 HIS 0.007 0.001 HIS d 30 Details of bonding type rmsd covalent geometry : bond 0.00326 (11711) covalent geometry : angle 0.67988 (16000) hydrogen bonds : bond 0.03617 ( 580) hydrogen bonds : angle 4.42278 ( 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 168 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.7900 (tt0) cc_final: 0.7645 (tt0) REVERT: A 40 GLN cc_start: 0.8583 (tp40) cc_final: 0.8307 (tp-100) REVERT: A 49 LEU cc_start: 0.9742 (mt) cc_final: 0.9533 (mt) REVERT: A 54 LYS cc_start: 0.8684 (ttpt) cc_final: 0.8279 (tmtt) REVERT: D 44 ASN cc_start: 0.9053 (OUTLIER) cc_final: 0.8784 (t0) REVERT: D 176 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9351 (mm) REVERT: D 202 LEU cc_start: 0.9657 (OUTLIER) cc_final: 0.9298 (tp) REVERT: E 63 MET cc_start: 0.8698 (ptm) cc_final: 0.8341 (tmm) REVERT: E 81 MET cc_start: 0.8684 (tmm) cc_final: 0.8094 (tmm) REVERT: E 124 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8485 (mtt) REVERT: E 192 HIS cc_start: 0.8448 (p90) cc_final: 0.8086 (p90) REVERT: a 43 SER cc_start: 0.9480 (OUTLIER) cc_final: 0.9213 (p) REVERT: e 6 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.7998 (mm) REVERT: e 22 LEU cc_start: 0.9083 (tp) cc_final: 0.8726 (tt) REVERT: e 285 LEU cc_start: 0.9782 (mp) cc_final: 0.9518 (mt) outliers start: 42 outliers final: 17 residues processed: 158 average time/residue: 0.1042 time to fit residues: 23.6451 Evaluate side-chains 128 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 44 ASN Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 180 TYR 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 126 VAL Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 261 GLN Chi-restraints excluded: chain a residue 43 SER 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 248 THR Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 20 LYS 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: 8.9990 chunk 7 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 120 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 ASN D 158 GLN D 257 HIS E 25 ASN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN E 230 HIS ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 89 HIS d 150 ASN B e 58 ASN ** e 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.043946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.033470 restraints weight = 143905.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.035064 restraints weight = 60162.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.036158 restraints weight = 35531.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.036879 restraints weight = 24869.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.037401 restraints weight = 19448.876| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11711 Z= 0.155 Angle : 0.660 13.251 16000 Z= 0.348 Chirality : 0.042 0.206 1782 Planarity : 0.004 0.049 1878 Dihedral : 18.396 82.089 1923 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.78 % Favored : 95.06 % Rotamer: Outliers : 3.97 % Allowed : 29.83 % Favored : 66.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.23), residues: 1321 helix: 0.81 (0.20), residues: 693 sheet: -1.78 (0.44), residues: 136 loop : -1.98 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG e 106 TYR 0.015 0.002 TYR d 284 PHE 0.021 0.002 PHE A 68 TRP 0.012 0.001 TRP D 218 HIS 0.007 0.001 HIS d 168 Details of bonding type rmsd covalent geometry : bond 0.00354 (11711) covalent geometry : angle 0.66034 (16000) hydrogen bonds : bond 0.03425 ( 580) hydrogen bonds : angle 4.22472 ( 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 : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8472 (mp0) cc_final: 0.8190 (pm20) REVERT: A 34 GLU cc_start: 0.7852 (tt0) cc_final: 0.7570 (tt0) REVERT: A 40 GLN cc_start: 0.8665 (tp40) cc_final: 0.8339 (tp-100) REVERT: A 54 LYS cc_start: 0.8748 (ttpt) cc_final: 0.8136 (tmtt) REVERT: D 176 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9364 (mm) REVERT: D 202 LEU cc_start: 0.9717 (OUTLIER) cc_final: 0.9301 (tp) REVERT: E 81 MET cc_start: 0.8792 (tmm) cc_final: 0.8174 (tmm) REVERT: E 124 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8599 (mtt) REVERT: E 192 HIS cc_start: 0.8513 (p90) cc_final: 0.8153 (p90) REVERT: a 20 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7800 (tt0) REVERT: a 43 SER cc_start: 0.9510 (OUTLIER) cc_final: 0.9250 (p) REVERT: e 22 LEU cc_start: 0.9073 (tp) cc_final: 0.8725 (tt) REVERT: e 30 HIS cc_start: 0.7849 (OUTLIER) cc_final: 0.6599 (m170) outliers start: 44 outliers final: 25 residues processed: 139 average time/residue: 0.1039 time to fit residues: 21.0559 Evaluate side-chains 125 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain D residue 19 CYS 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 176 LEU Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain D residue 192 HIS 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 217 LEU Chi-restraints excluded: chain E residue 261 GLN 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 87 ILE Chi-restraints excluded: chain d residue 192 HIS Chi-restraints excluded: chain d residue 233 THR Chi-restraints excluded: chain d residue 275 TYR 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 180 TYR Chi-restraints excluded: chain e residue 192 HIS Chi-restraints excluded: chain e residue 256 PHE Chi-restraints excluded: chain e residue 266 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 115 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 48 optimal weight: 8.9990 chunk 87 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 46 GLN ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 158 GLN ** e 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 199 ASN ** 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 = 0.3089 r_free = 0.3089 target = 0.042460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.031806 restraints weight = 174788.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.033457 restraints weight = 63471.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.034592 restraints weight = 35655.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.035349 restraints weight = 24322.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.035839 restraints weight = 18740.621| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11711 Z= 0.171 Angle : 0.661 13.715 16000 Z= 0.348 Chirality : 0.043 0.260 1782 Planarity : 0.004 0.047 1878 Dihedral : 18.311 81.622 1922 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.39 % Favored : 94.46 % Rotamer: Outliers : 4.06 % Allowed : 28.77 % Favored : 67.17 % 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 aren not related in a simple way. whole: -0.59 (0.23), residues: 1321 helix: 0.95 (0.20), residues: 699 sheet: -1.81 (0.44), residues: 136 loop : -1.94 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG e 270 TYR 0.015 0.002 TYR e 100 PHE 0.025 0.002 PHE E 152 TRP 0.011 0.002 TRP D 218 HIS 0.006 0.001 HIS d 168 Details of bonding type rmsd covalent geometry : bond 0.00386 (11711) covalent geometry : angle 0.66081 (16000) hydrogen bonds : bond 0.03418 ( 580) hydrogen bonds : angle 4.12868 ( 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 145 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 100 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8680 (mp0) cc_final: 0.8351 (pm20) REVERT: A 34 GLU cc_start: 0.8013 (tt0) cc_final: 0.7685 (tt0) REVERT: A 40 GLN cc_start: 0.8819 (tp40) cc_final: 0.8573 (tp-100) REVERT: D 124 MET cc_start: 0.9100 (mtp) cc_final: 0.8636 (mtp) REVERT: D 176 LEU cc_start: 0.9625 (OUTLIER) cc_final: 0.9393 (mm) REVERT: D 202 LEU cc_start: 0.9722 (OUTLIER) cc_final: 0.9314 (tp) REVERT: D 261 GLN cc_start: 0.8415 (mp10) cc_final: 0.8212 (mp10) REVERT: E 124 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8722 (mtt) REVERT: E 182 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8178 (tt) REVERT: a 20 GLU cc_start: 0.8482 (mt-10) cc_final: 0.7853 (tt0) REVERT: a 43 SER cc_start: 0.9538 (OUTLIER) cc_final: 0.9300 (p) REVERT: e 30 HIS cc_start: 0.8093 (OUTLIER) cc_final: 0.7140 (m170) REVERT: e 101 MET cc_start: 0.9014 (tpt) cc_final: 0.8799 (tpt) REVERT: e 125 ARG cc_start: 0.9185 (tpp80) cc_final: 0.8962 (mmm-85) outliers start: 45 outliers final: 24 residues processed: 138 average time/residue: 0.1096 time to fit residues: 21.8582 Evaluate side-chains 124 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain D residue 192 HIS 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 182 LEU 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 192 HIS Chi-restraints excluded: chain d residue 275 TYR 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 158 GLN Chi-restraints excluded: chain e residue 180 TYR 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: 9.9990 chunk 108 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 96 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.042890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.032474 restraints weight = 121257.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.033993 restraints weight = 52990.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.035017 restraints weight = 32067.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.035686 restraints weight = 22920.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.036160 restraints weight = 18282.109| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.4722 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= 0.151 Angle : 0.685 19.019 16000 Z= 0.352 Chirality : 0.043 0.242 1782 Planarity : 0.004 0.048 1878 Dihedral : 18.243 82.910 1916 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.71 % Favored : 95.14 % Rotamer: Outliers : 3.35 % Allowed : 29.30 % Favored : 67.34 % 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 aren not related in a simple way. whole: -0.46 (0.23), residues: 1321 helix: 1.03 (0.20), residues: 701 sheet: -1.72 (0.46), residues: 136 loop : -1.87 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG e 270 TYR 0.017 0.001 TYR e 100 PHE 0.020 0.002 PHE A 68 TRP 0.010 0.001 TRP D 218 HIS 0.006 0.001 HIS d 168 Details of bonding type rmsd covalent geometry : bond 0.00346 (11711) covalent geometry : angle 0.68499 (16000) hydrogen bonds : bond 0.03342 ( 580) hydrogen bonds : angle 4.09452 ( 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 135 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 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 20 GLU cc_start: 0.8675 (mp0) cc_final: 0.8326 (pm20) REVERT: A 34 GLU cc_start: 0.8077 (tt0) cc_final: 0.7712 (tt0) REVERT: A 40 GLN cc_start: 0.8871 (tp40) cc_final: 0.8501 (tp-100) REVERT: D 124 MET cc_start: 0.9178 (mtp) cc_final: 0.8756 (mtp) REVERT: D 176 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9406 (mm) REVERT: D 202 LEU cc_start: 0.9705 (OUTLIER) cc_final: 0.9308 (tp) REVERT: E 63 MET cc_start: 0.8708 (ptm) cc_final: 0.8399 (tmm) REVERT: E 124 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8766 (mtt) REVERT: a 43 SER cc_start: 0.9479 (OUTLIER) cc_final: 0.9262 (p) REVERT: d 61 MET cc_start: 0.9398 (tpp) cc_final: 0.9163 (tpt) REVERT: e 22 LEU cc_start: 0.9117 (tp) cc_final: 0.8899 (tt) REVERT: e 30 HIS cc_start: 0.8099 (OUTLIER) cc_final: 0.7521 (m170) REVERT: e 101 MET cc_start: 0.9050 (tpt) cc_final: 0.8785 (tpt) REVERT: e 106 ARG cc_start: 0.9451 (mmt90) cc_final: 0.9049 (mmt90) REVERT: e 254 LEU cc_start: 0.9670 (OUTLIER) cc_final: 0.9246 (mt) outliers start: 37 outliers final: 20 residues processed: 127 average time/residue: 0.1024 time to fit residues: 18.9894 Evaluate side-chains 116 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain D residue 192 HIS 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 217 LEU Chi-restraints excluded: chain a residue 43 SER Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 81 MET Chi-restraints excluded: chain d residue 101 MET 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 180 TYR Chi-restraints excluded: chain e residue 254 LEU 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: 0.9990 chunk 41 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 279 ASN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 36 ASN ** e 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.043208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.032502 restraints weight = 166366.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.034166 restraints weight = 61754.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.035306 restraints weight = 34912.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.036078 restraints weight = 23887.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.036586 restraints weight = 18378.044| |-----------------------------------------------------------------------------| r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11711 Z= 0.141 Angle : 0.687 19.085 16000 Z= 0.351 Chirality : 0.043 0.226 1782 Planarity : 0.004 0.048 1878 Dihedral : 18.144 82.963 1916 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.94 % Favored : 94.99 % Rotamer: Outliers : 2.82 % Allowed : 29.66 % Favored : 67.52 % 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 aren not related in a simple way. whole: -0.33 (0.23), residues: 1321 helix: 1.13 (0.20), residues: 701 sheet: -1.68 (0.49), residues: 121 loop : -1.79 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG e 270 TYR 0.019 0.001 TYR d 275 PHE 0.022 0.002 PHE E 152 TRP 0.009 0.001 TRP D 218 HIS 0.006 0.001 HIS d 168 Details of bonding type rmsd covalent geometry : bond 0.00327 (11711) covalent geometry : angle 0.68728 (16000) hydrogen bonds : bond 0.03282 ( 580) hydrogen bonds : angle 4.02352 ( 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 131 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8619 (mp0) cc_final: 0.8269 (pm20) REVERT: A 34 GLU cc_start: 0.8073 (tt0) cc_final: 0.7755 (tt0) REVERT: A 40 GLN cc_start: 0.8866 (tp40) cc_final: 0.8477 (tp-100) REVERT: D 124 MET cc_start: 0.9209 (mtp) cc_final: 0.8809 (mtp) REVERT: D 176 LEU cc_start: 0.9643 (OUTLIER) cc_final: 0.9408 (mm) REVERT: D 202 LEU cc_start: 0.9701 (OUTLIER) cc_final: 0.9309 (tp) REVERT: E 263 MET cc_start: 0.9090 (pmm) cc_final: 0.8604 (pmm) REVERT: a 20 GLU cc_start: 0.8502 (mt-10) cc_final: 0.7899 (tt0) REVERT: a 43 SER cc_start: 0.9500 (OUTLIER) cc_final: 0.9287 (p) REVERT: d 61 MET cc_start: 0.9412 (tpp) cc_final: 0.9144 (tpt) REVERT: d 263 MET cc_start: 0.9175 (mtp) cc_final: 0.8914 (ptp) REVERT: e 101 MET cc_start: 0.9086 (tpt) cc_final: 0.8841 (tpt) REVERT: e 254 LEU cc_start: 0.9664 (OUTLIER) cc_final: 0.9243 (mt) outliers start: 31 outliers final: 20 residues processed: 126 average time/residue: 0.0852 time to fit residues: 16.0214 Evaluate side-chains 115 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain D residue 192 HIS Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 98 THR 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 81 MET Chi-restraints excluded: chain d residue 101 MET Chi-restraints excluded: chain d residue 192 HIS Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 34 ASP Chi-restraints excluded: chain e residue 57 THR Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 180 TYR Chi-restraints excluded: chain e residue 254 LEU 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: 8.9990 chunk 121 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 69 optimal weight: 9.9990 chunk 43 optimal weight: 0.0470 chunk 116 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 GLN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 2 GLN e 158 GLN ** e 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 199 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 = 0.3125 r_free = 0.3125 target = 0.043590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.033016 restraints weight = 155177.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.034636 restraints weight = 60199.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.035748 restraints weight = 34440.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.036503 restraints weight = 23730.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.037004 restraints weight = 18375.499| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11711 Z= 0.136 Angle : 0.678 18.876 16000 Z= 0.347 Chirality : 0.043 0.220 1782 Planarity : 0.003 0.047 1878 Dihedral : 18.062 82.623 1916 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.56 % Favored : 95.37 % Rotamer: Outliers : 2.65 % Allowed : 29.39 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.23), residues: 1321 helix: 1.21 (0.20), residues: 701 sheet: -1.50 (0.50), residues: 119 loop : -1.70 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG d 18 TYR 0.018 0.001 TYR e 198 PHE 0.017 0.001 PHE A 68 TRP 0.009 0.001 TRP D 218 HIS 0.006 0.001 HIS d 168 Details of bonding type rmsd covalent geometry : bond 0.00315 (11711) covalent geometry : angle 0.67823 (16000) hydrogen bonds : bond 0.03232 ( 580) hydrogen bonds : angle 3.99118 ( 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 127 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8090 (tt0) cc_final: 0.7721 (tt0) REVERT: A 40 GLN cc_start: 0.8819 (tp40) cc_final: 0.8498 (tp-100) REVERT: D 124 MET cc_start: 0.9240 (mtp) cc_final: 0.8854 (mtp) REVERT: D 202 LEU cc_start: 0.9692 (OUTLIER) cc_final: 0.9301 (tp) REVERT: E 9 GLN cc_start: 0.7818 (mp10) cc_final: 0.7614 (mp10) REVERT: E 63 MET cc_start: 0.8689 (ptm) cc_final: 0.8447 (tmm) REVERT: a 43 SER cc_start: 0.9504 (OUTLIER) cc_final: 0.9298 (p) REVERT: a 54 LYS cc_start: 0.8711 (mmtt) cc_final: 0.8476 (mmmt) REVERT: a 75 MET cc_start: 0.7918 (tmm) cc_final: 0.7387 (tmm) REVERT: d 61 MET cc_start: 0.9399 (tpp) cc_final: 0.9117 (tpt) REVERT: d 263 MET cc_start: 0.9137 (mtp) cc_final: 0.8911 (ptp) REVERT: e 101 MET cc_start: 0.9052 (tpt) cc_final: 0.8769 (mmm) REVERT: e 254 LEU cc_start: 0.9661 (OUTLIER) cc_final: 0.9249 (mt) outliers start: 29 outliers final: 16 residues processed: 122 average time/residue: 0.1064 time to fit residues: 19.1329 Evaluate side-chains 113 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 180 TYR 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 217 LEU Chi-restraints excluded: chain a residue 43 SER Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 57 THR Chi-restraints excluded: chain e residue 180 TYR Chi-restraints excluded: chain e residue 254 LEU 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: 7.9990 chunk 2 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.042893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.032920 restraints weight = 117325.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.034374 restraints weight = 51278.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.035360 restraints weight = 30889.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.036034 restraints weight = 21974.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.036496 restraints weight = 17376.619| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11711 Z= 0.155 Angle : 0.722 19.564 16000 Z= 0.366 Chirality : 0.043 0.212 1782 Planarity : 0.004 0.045 1878 Dihedral : 18.061 83.624 1916 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.63 % Favored : 95.29 % Rotamer: Outliers : 2.29 % Allowed : 30.10 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.23), residues: 1321 helix: 1.23 (0.20), residues: 701 sheet: -1.39 (0.50), residues: 119 loop : -1.63 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG e 270 TYR 0.015 0.001 TYR d 275 PHE 0.018 0.002 PHE A 68 TRP 0.009 0.001 TRP D 218 HIS 0.006 0.001 HIS d 168 Details of bonding type rmsd covalent geometry : bond 0.00359 (11711) covalent geometry : angle 0.72187 (16000) hydrogen bonds : bond 0.03300 ( 580) hydrogen bonds : angle 4.03203 ( 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 119 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8130 (tt0) cc_final: 0.7736 (tt0) REVERT: A 40 GLN cc_start: 0.8839 (tp40) cc_final: 0.8562 (tp-100) REVERT: D 1 MET cc_start: 0.6387 (tpp) cc_final: 0.5811 (mtp) REVERT: D 124 MET cc_start: 0.9259 (mtp) cc_final: 0.8881 (mtp) REVERT: D 176 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9398 (mm) REVERT: D 202 LEU cc_start: 0.9698 (OUTLIER) cc_final: 0.9309 (tp) REVERT: E 9 GLN cc_start: 0.7793 (mp10) cc_final: 0.7574 (mp10) REVERT: E 63 MET cc_start: 0.8653 (ptm) cc_final: 0.8378 (tmm) REVERT: a 34 GLU cc_start: 0.8018 (tt0) cc_final: 0.7558 (tt0) REVERT: a 75 MET cc_start: 0.7878 (tmm) cc_final: 0.7318 (tmm) REVERT: d 61 MET cc_start: 0.9423 (tpp) cc_final: 0.9148 (tpt) REVERT: d 263 MET cc_start: 0.9138 (mtp) cc_final: 0.8892 (ptp) REVERT: e 30 HIS cc_start: 0.8367 (OUTLIER) cc_final: 0.7582 (m170) REVERT: e 101 MET cc_start: 0.9056 (tpt) cc_final: 0.8769 (mmm) REVERT: e 254 LEU cc_start: 0.9662 (OUTLIER) cc_final: 0.9257 (mt) outliers start: 25 outliers final: 17 residues processed: 114 average time/residue: 0.1020 time to fit residues: 17.4944 Evaluate side-chains 109 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain D residue 192 HIS 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 217 LEU Chi-restraints excluded: chain d residue 39 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 122 LEU Chi-restraints excluded: chain e residue 180 TYR Chi-restraints excluded: chain e residue 254 LEU 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: 0.3980 chunk 37 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 35 optimal weight: 0.0670 overall best weight: 1.2522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.042904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.032772 restraints weight = 133977.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.034275 restraints weight = 55329.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.035308 restraints weight = 32453.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.036002 restraints weight = 22705.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.036497 restraints weight = 17782.587| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11711 Z= 0.153 Angle : 0.716 19.972 16000 Z= 0.365 Chirality : 0.043 0.198 1782 Planarity : 0.004 0.045 1878 Dihedral : 18.055 84.190 1916 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.63 % Favored : 95.29 % Rotamer: Outliers : 2.03 % Allowed : 30.19 % Favored : 67.78 % 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 aren not related in a simple way. whole: -0.09 (0.23), residues: 1321 helix: 1.24 (0.20), residues: 701 sheet: -1.42 (0.47), residues: 131 loop : -1.60 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG e 270 TYR 0.014 0.001 TYR e 198 PHE 0.018 0.002 PHE A 68 TRP 0.010 0.001 TRP D 218 HIS 0.005 0.001 HIS d 168 Details of bonding type rmsd covalent geometry : bond 0.00354 (11711) covalent geometry : angle 0.71637 (16000) hydrogen bonds : bond 0.03296 ( 580) hydrogen bonds : angle 4.05127 ( 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 110 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8145 (tt0) cc_final: 0.7769 (tt0) REVERT: A 40 GLN cc_start: 0.8869 (tp40) cc_final: 0.8591 (tp-100) REVERT: D 1 MET cc_start: 0.6386 (tpp) cc_final: 0.5749 (mtp) REVERT: D 124 MET cc_start: 0.9263 (mtp) cc_final: 0.8889 (mtp) REVERT: D 176 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9397 (mm) REVERT: D 202 LEU cc_start: 0.9698 (OUTLIER) cc_final: 0.9307 (tp) REVERT: E 9 GLN cc_start: 0.7790 (mp10) cc_final: 0.7555 (mp10) REVERT: E 63 MET cc_start: 0.8659 (ptm) cc_final: 0.8367 (tmm) REVERT: a 34 GLU cc_start: 0.8015 (tt0) cc_final: 0.7557 (tt0) REVERT: a 75 MET cc_start: 0.7817 (tmm) cc_final: 0.7240 (tmm) REVERT: d 61 MET cc_start: 0.9422 (tpp) cc_final: 0.9140 (tpt) REVERT: d 263 MET cc_start: 0.9144 (mtp) cc_final: 0.8904 (ptp) REVERT: e 13 MET cc_start: 0.8684 (tpp) cc_final: 0.8101 (tpp) REVERT: e 30 HIS cc_start: 0.8351 (OUTLIER) cc_final: 0.7569 (m170) REVERT: e 254 LEU cc_start: 0.9654 (OUTLIER) cc_final: 0.9245 (mt) outliers start: 22 outliers final: 17 residues processed: 106 average time/residue: 0.0975 time to fit residues: 15.7354 Evaluate side-chains 107 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain D residue 192 HIS 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 217 LEU Chi-restraints excluded: chain d residue 39 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 122 LEU Chi-restraints excluded: chain e residue 180 TYR Chi-restraints excluded: chain e residue 254 LEU 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: 2.9990 chunk 71 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 117 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 61 ASN ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.041731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.031325 restraints weight = 143763.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.032837 restraints weight = 57649.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.033889 restraints weight = 33783.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.034603 restraints weight = 23676.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.035076 restraints weight = 18595.594| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11711 Z= 0.195 Angle : 0.731 19.586 16000 Z= 0.375 Chirality : 0.044 0.200 1782 Planarity : 0.004 0.042 1878 Dihedral : 18.120 86.669 1916 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.32 % Favored : 94.61 % Rotamer: Outliers : 2.12 % Allowed : 30.10 % Favored : 67.78 % 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 aren not related in a simple way. whole: -0.19 (0.23), residues: 1321 helix: 1.14 (0.20), residues: 713 sheet: -1.47 (0.46), residues: 136 loop : -1.65 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG e 270 TYR 0.017 0.002 TYR D 100 PHE 0.020 0.002 PHE A 68 TRP 0.011 0.002 TRP D 218 HIS 0.006 0.001 HIS d 168 Details of bonding type rmsd covalent geometry : bond 0.00444 (11711) covalent geometry : angle 0.73141 (16000) hydrogen bonds : bond 0.03551 ( 580) hydrogen bonds : angle 4.14898 ( 1676) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1896.88 seconds wall clock time: 33 minutes 47.48 seconds (2027.48 seconds total)