Starting phenix.real_space_refine on Thu Jul 2 11:39:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ihi_35445/07_2026/8ihi_35445.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihi_35445/07_2026/8ihi_35445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ihi_35445/07_2026/8ihi_35445.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihi_35445/07_2026/8ihi_35445.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ihi_35445/07_2026/8ihi_35445.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ihi_35445/07_2026/8ihi_35445.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ihi_35445/07_2026/8ihi_35445.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihi_35445/07_2026/8ihi_35445.cif" } resolution = 3.11 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= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5545 2.51 5 N 1472 2.21 5 O 1591 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8665 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1695 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 1, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 30 Chain: "S" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1706 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2477 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 6, 'GLN:plan1': 5, 'ARG:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 91 Chain: "C" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 376 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "R" Number of atoms: 2381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2381 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 281} 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: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 1, 'P9X': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.76, per 1000 atoms: 0.20 Number of scatterers: 8665 At special positions: 0 Unit cell: (89.1, 117.81, 135.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1591 8.00 N 1472 7.00 C 5545 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.86 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " distance=2.03 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 Links applied NAG-ASN " NAG R 601 " - " ASN R 17 " Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 333.4 milliseconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 15 sheets defined 36.4% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.517A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.718A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.293A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.726A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.523A pdb=" N LYS A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.973A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.534A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.545A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU C 22 " --> pdb=" O GLN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.581A pdb=" N ASP C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'R' and resid 24 through 55 removed outlier: 3.842A pdb=" N LYS R 28 " --> pdb=" O ASP R 24 " (cutoff:3.500A) Proline residue: R 31 - end of helix removed outlier: 3.520A pdb=" N LEU R 36 " --> pdb=" O PRO R 32 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE R 38 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU R 43 " --> pdb=" O ILE R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 78 removed outlier: 3.548A pdb=" N ILE R 78 " --> pdb=" O PHE R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 89 removed outlier: 3.529A pdb=" N ASN R 86 " --> pdb=" O PHE R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 128 removed outlier: 3.863A pdb=" N LEU R 107 " --> pdb=" O MET R 103 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG R 111 " --> pdb=" O LEU R 107 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N VAL R 121 " --> pdb=" O PHE R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 139 removed outlier: 3.798A pdb=" N ILE R 139 " --> pdb=" O LEU R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 158 Processing helix chain 'R' and resid 159 through 163 Processing helix chain 'R' and resid 187 through 218 removed outlier: 4.064A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU R 199 " --> pdb=" O LEU R 195 " (cutoff:3.500A) Proline residue: R 200 - end of helix Processing helix chain 'R' and resid 223 through 261 removed outlier: 3.536A pdb=" N PHE R 232 " --> pdb=" O ARG R 228 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET R 234 " --> pdb=" O ILE R 230 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 269 through 281 removed outlier: 3.615A pdb=" N LEU R 274 " --> pdb=" O ARG R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 295 removed outlier: 3.827A pdb=" N ASN R 286 " --> pdb=" O PHE R 282 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER R 287 " --> pdb=" O THR R 283 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.683A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'S' and resid 6 through 7 removed outlier: 3.715A pdb=" N SER S 7 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 58 through 60 removed outlier: 3.538A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 45 through 46 removed outlier: 3.582A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S' and resid 155 through 160 Processing sheet with id=AA6, first strand: chain 'S' and resid 194 through 195 removed outlier: 5.383A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR S 227 " --> pdb=" O THR S 243 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.720A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.738A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.616A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.781A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.815A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.465A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.559A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 10 through 12 removed outlier: 3.962A pdb=" N ILE R 182 " --> pdb=" O CYS R 19 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 169 through 171 removed outlier: 3.584A pdb=" N ILE R 169 " --> pdb=" O LEU R 176 " (cutoff:3.500A) 404 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.33 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2784 1.34 - 1.46: 2206 1.46 - 1.58: 3792 1.58 - 1.70: 0 1.70 - 1.82: 79 Bond restraints: 8861 Sorted by residual: bond pdb=" C5 P9X R 602 " pdb=" O2 P9X R 602 " ideal model delta sigma weight residual 1.250 1.306 -0.056 2.00e-02 2.50e+03 7.81e+00 bond pdb=" C4 P9X R 602 " pdb=" C5 P9X R 602 " ideal model delta sigma weight residual 1.530 1.476 0.054 2.00e-02 2.50e+03 7.34e+00 bond pdb=" CA LYS R 165 " pdb=" C LYS R 165 " ideal model delta sigma weight residual 1.523 1.494 0.029 1.24e-02 6.50e+03 5.43e+00 bond pdb=" N LYS R 165 " pdb=" CA LYS R 165 " ideal model delta sigma weight residual 1.455 1.432 0.024 1.22e-02 6.72e+03 3.83e+00 bond pdb=" CB PRO S 151 " pdb=" CG PRO S 151 " ideal model delta sigma weight residual 1.492 1.569 -0.077 5.00e-02 4.00e+02 2.40e+00 ... (remaining 8856 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 11912 2.16 - 4.33: 106 4.33 - 6.49: 15 6.49 - 8.65: 3 8.65 - 10.81: 2 Bond angle restraints: 12038 Sorted by residual: angle pdb=" CB MET R 167 " pdb=" CG MET R 167 " pdb=" SD MET R 167 " ideal model delta sigma weight residual 112.70 123.51 -10.81 3.00e+00 1.11e-01 1.30e+01 angle pdb=" CA PRO S 151 " pdb=" N PRO S 151 " pdb=" CD PRO S 151 " ideal model delta sigma weight residual 112.00 107.01 4.99 1.40e+00 5.10e-01 1.27e+01 angle pdb=" C ASP R 97 " pdb=" N ILE R 98 " pdb=" CA ILE R 98 " ideal model delta sigma weight residual 120.33 122.69 -2.36 8.00e-01 1.56e+00 8.73e+00 angle pdb=" CA LEU A 283 " pdb=" CB LEU A 283 " pdb=" CG LEU A 283 " ideal model delta sigma weight residual 116.30 125.82 -9.52 3.50e+00 8.16e-02 7.41e+00 angle pdb=" CA LEU R 47 " pdb=" CB LEU R 47 " pdb=" CG LEU R 47 " ideal model delta sigma weight residual 116.30 124.60 -8.30 3.50e+00 8.16e-02 5.62e+00 ... (remaining 12033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4478 17.92 - 35.84: 543 35.84 - 53.77: 136 53.77 - 71.69: 29 71.69 - 89.61: 5 Dihedral angle restraints: 5191 sinusoidal: 1915 harmonic: 3276 Sorted by residual: dihedral pdb=" CB CYS R 100 " pdb=" SG CYS R 100 " pdb=" SG CYS R 177 " pdb=" CB CYS R 177 " ideal model delta sinusoidal sigma weight residual -86.00 -138.25 52.25 1 1.00e+01 1.00e-02 3.72e+01 dihedral pdb=" CA PHE R 117 " pdb=" C PHE R 117 " pdb=" N LEU R 118 " pdb=" CA LEU R 118 " ideal model delta harmonic sigma weight residual 180.00 155.66 24.34 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CB CYS R 19 " pdb=" SG CYS R 19 " pdb=" SG CYS R 266 " pdb=" CB CYS R 266 " ideal model delta sinusoidal sigma weight residual -86.00 -55.41 -30.59 1 1.00e+01 1.00e-02 1.34e+01 ... (remaining 5188 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 804 0.027 - 0.054: 360 0.054 - 0.080: 120 0.080 - 0.107: 67 0.107 - 0.134: 27 Chirality restraints: 1378 Sorted by residual: chirality pdb=" CA VAL S 147 " pdb=" N VAL S 147 " pdb=" C VAL S 147 " pdb=" CB VAL S 147 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ASP S 90 " pdb=" N ASP S 90 " pdb=" C ASP S 90 " pdb=" CB ASP S 90 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 1375 not shown) Planarity restraints: 1523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR S 150 " -0.082 5.00e-02 4.00e+02 1.22e-01 2.39e+01 pdb=" N PRO S 151 " 0.211 5.00e-02 4.00e+02 pdb=" CA PRO S 151 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO S 151 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO R 31 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.32e+00 pdb=" N PRO R 32 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO R 32 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 32 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 52 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO C 53 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 53 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 53 " -0.027 5.00e-02 4.00e+02 ... (remaining 1520 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1386 2.76 - 3.29: 7952 3.29 - 3.83: 13782 3.83 - 4.36: 16840 4.36 - 4.90: 29890 Nonbonded interactions: 69850 Sorted by model distance: nonbonded pdb=" O LEU R 280 " pdb=" OG1 THR R 283 " model vdw 2.221 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.226 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.239 3.040 nonbonded pdb=" O GLY R 262 " pdb=" OH TYR R 269 " model vdw 2.255 3.040 nonbonded pdb=" O LEU R 257 " pdb=" OG SER R 261 " model vdw 2.264 3.040 ... (remaining 69845 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.900 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 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 0.831 8866 Z= 0.460 Angle : 0.538 10.813 12049 Z= 0.276 Chirality : 0.040 0.134 1378 Planarity : 0.005 0.122 1522 Dihedral : 16.775 89.608 3061 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.22 % Allowed : 25.98 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.25), residues: 1115 helix: 0.14 (0.28), residues: 352 sheet: -0.02 (0.31), residues: 269 loop : -0.92 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 18 TYR 0.021 0.001 TYR S 235 PHE 0.026 0.001 PHE R 38 TRP 0.006 0.001 TRP R 152 HIS 0.002 0.000 HIS R 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 8861) covalent geometry : angle 0.53199 / 0.27 (12038) SS BOND : bond 0.41533 / 21.86 ( 4) SS BOND : angle 3.10052 / 1.64 ( 8) hydrogen bonds : bond 0.27149 / 18.60 ( 404) hydrogen bonds : angle 8.26752 / 5.79 ( 1131) link_NAG-ASN : bond 0.00076 / 0.04 ( 1) link_NAG-ASN : angle 0.80151 / 0.44 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 144 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: S 69 THR cc_start: 0.8404 (t) cc_final: 0.8071 (m) REVERT: S 87 ARG cc_start: 0.7915 (mtt180) cc_final: 0.7526 (mtm-85) REVERT: C 42 GLU cc_start: 0.7684 (mp0) cc_final: 0.7262 (mp0) outliers start: 2 outliers final: 2 residues processed: 145 average time/residue: 0.0798 time to fit residues: 16.0851 Evaluate side-chains 136 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain R residue 272 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 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 = 0.3887 r_free = 0.3887 target = 0.151476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.118115 restraints weight = 11167.800| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.44 r_work: 0.3383 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8866 Z= 0.122 Angle : 0.556 8.196 12049 Z= 0.291 Chirality : 0.042 0.146 1378 Planarity : 0.005 0.082 1522 Dihedral : 4.288 32.960 1238 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.56 % Allowed : 23.86 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.25), residues: 1115 helix: 1.43 (0.27), residues: 360 sheet: 0.25 (0.32), residues: 261 loop : -0.85 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 18 TYR 0.021 0.001 TYR S 235 PHE 0.012 0.001 PHE A 274 TRP 0.010 0.001 TRP B 169 HIS 0.002 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 8861) covalent geometry : angle 0.55533 / 0.29 (12038) SS BOND : bond 0.00517 / 0.27 ( 4) SS BOND : angle 0.83258 / 0.47 ( 8) hydrogen bonds : bond 0.05048 / 3.42 ( 404) hydrogen bonds : angle 4.91050 / 3.41 ( 1131) link_NAG-ASN : bond 0.00180 / 0.09 ( 1) link_NAG-ASN : angle 1.40876 / 0.79 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8130 (t0) cc_final: 0.7807 (m-30) REVERT: A 24 ARG cc_start: 0.7431 (mtm110) cc_final: 0.7163 (ttp-110) REVERT: S 87 ARG cc_start: 0.7875 (mtt180) cc_final: 0.7434 (mtm-85) REVERT: S 202 ARG cc_start: 0.8342 (mtm110) cc_final: 0.8078 (mtm110) REVERT: R 167 MET cc_start: 0.5841 (tpp) cc_final: 0.5386 (tpp) outliers start: 23 outliers final: 10 residues processed: 153 average time/residue: 0.0846 time to fit residues: 17.7531 Evaluate side-chains 140 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 268 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 69 optimal weight: 8.9990 chunk 43 optimal weight: 20.0000 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 8 optimal weight: 0.0770 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 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 = 0.3933 r_free = 0.3933 target = 0.156135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.122153 restraints weight = 11235.760| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.51 r_work: 0.3399 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8866 Z= 0.100 Angle : 0.500 8.399 12049 Z= 0.260 Chirality : 0.041 0.141 1378 Planarity : 0.004 0.065 1522 Dihedral : 3.993 28.384 1235 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.56 % Allowed : 24.75 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.26), residues: 1115 helix: 1.97 (0.27), residues: 360 sheet: 0.22 (0.32), residues: 277 loop : -0.85 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 18 TYR 0.023 0.001 TYR S 235 PHE 0.017 0.001 PHE R 38 TRP 0.008 0.001 TRP B 339 HIS 0.002 0.000 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 ( 8861) covalent geometry : angle 0.49930 / 0.26 (12038) SS BOND : bond 0.00307 / 0.16 ( 4) SS BOND : angle 0.63953 / 0.35 ( 8) hydrogen bonds : bond 0.04052 / 2.78 ( 404) hydrogen bonds : angle 4.34263 / 3.01 ( 1131) link_NAG-ASN : bond 0.00144 / 0.08 ( 1) link_NAG-ASN : angle 1.52342 / 0.84 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.246 Fit side-chains REVERT: A 197 LYS cc_start: 0.8723 (mmtm) cc_final: 0.8269 (mtmt) REVERT: S 202 ARG cc_start: 0.8307 (mtm110) cc_final: 0.8054 (mtm110) REVERT: B 137 ARG cc_start: 0.8100 (tpt90) cc_final: 0.7712 (tpp80) REVERT: R 14 ASP cc_start: 0.7015 (m-30) cc_final: 0.6768 (t0) REVERT: R 47 LEU cc_start: 0.8154 (tt) cc_final: 0.7885 (mp) outliers start: 23 outliers final: 11 residues processed: 150 average time/residue: 0.0935 time to fit residues: 18.9984 Evaluate side-chains 135 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 263 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 47 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.154182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.119895 restraints weight = 11474.932| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.54 r_work: 0.3372 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8866 Z= 0.127 Angle : 0.511 8.400 12049 Z= 0.266 Chirality : 0.041 0.158 1378 Planarity : 0.004 0.057 1522 Dihedral : 4.028 23.298 1235 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.12 % Allowed : 24.75 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.26), residues: 1115 helix: 2.09 (0.28), residues: 360 sheet: 0.25 (0.32), residues: 271 loop : -0.88 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.019 0.001 TYR S 235 PHE 0.021 0.001 PHE R 38 TRP 0.008 0.001 TRP S 47 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 8861) covalent geometry : angle 0.51065 / 0.27 (12038) SS BOND : bond 0.00245 / 0.13 ( 4) SS BOND : angle 0.53268 / 0.30 ( 8) hydrogen bonds : bond 0.03901 / 2.67 ( 404) hydrogen bonds : angle 4.17614 / 2.89 ( 1131) link_NAG-ASN : bond 0.00039 / 0.02 ( 1) link_NAG-ASN : angle 1.64444 / 0.91 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.325 Fit side-chains REVERT: S 202 ARG cc_start: 0.8307 (mtm110) cc_final: 0.8041 (mtm110) REVERT: B 137 ARG cc_start: 0.8263 (tpt90) cc_final: 0.7663 (tpp-160) REVERT: R 14 ASP cc_start: 0.7326 (m-30) cc_final: 0.7014 (t0) REVERT: R 47 LEU cc_start: 0.8263 (tt) cc_final: 0.8005 (mp) REVERT: R 150 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7932 (tt) REVERT: R 190 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6858 (mm-30) outliers start: 28 outliers final: 16 residues processed: 151 average time/residue: 0.0924 time to fit residues: 19.2143 Evaluate side-chains 142 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 190 GLU Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 268 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 107 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 108 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 81 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 69 optimal weight: 0.1980 chunk 90 optimal weight: 9.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.155245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.120977 restraints weight = 11390.607| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.53 r_work: 0.3383 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8866 Z= 0.107 Angle : 0.495 8.825 12049 Z= 0.257 Chirality : 0.041 0.134 1378 Planarity : 0.004 0.049 1522 Dihedral : 3.918 20.628 1235 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.90 % Allowed : 24.86 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.26), residues: 1115 helix: 2.26 (0.28), residues: 361 sheet: 0.21 (0.31), residues: 279 loop : -0.86 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 270 TYR 0.022 0.001 TYR S 235 PHE 0.023 0.001 PHE R 38 TRP 0.007 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 8861) covalent geometry : angle 0.49452 / 0.26 (12038) SS BOND : bond 0.00222 / 0.12 ( 4) SS BOND : angle 0.48556 / 0.28 ( 8) hydrogen bonds : bond 0.03572 / 2.45 ( 404) hydrogen bonds : angle 4.04522 / 2.80 ( 1131) link_NAG-ASN : bond 0.00089 / 0.05 ( 1) link_NAG-ASN : angle 1.61266 / 0.90 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.301 Fit side-chains REVERT: S 140 MET cc_start: 0.8999 (mmm) cc_final: 0.8684 (mmm) REVERT: S 186 GLN cc_start: 0.8558 (pt0) cc_final: 0.8274 (pt0) REVERT: B 137 ARG cc_start: 0.8091 (tpt90) cc_final: 0.7594 (tpp-160) REVERT: R 150 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7867 (tt) REVERT: R 190 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.6523 (mm-30) REVERT: R 217 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7458 (tt0) outliers start: 26 outliers final: 16 residues processed: 151 average time/residue: 0.0815 time to fit residues: 17.0162 Evaluate side-chains 143 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 190 GLU Chi-restraints excluded: chain R residue 217 GLN Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 263 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 83 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 43 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 54 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 HIS B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.150809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.116686 restraints weight = 11430.813| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.49 r_work: 0.3305 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8866 Z= 0.214 Angle : 0.583 8.495 12049 Z= 0.305 Chirality : 0.044 0.197 1378 Planarity : 0.004 0.050 1522 Dihedral : 4.468 17.972 1235 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.68 % Allowed : 25.42 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.26), residues: 1115 helix: 1.91 (0.28), residues: 361 sheet: 0.19 (0.32), residues: 268 loop : -1.02 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 270 TYR 0.026 0.002 TYR S 235 PHE 0.025 0.002 PHE R 38 TRP 0.008 0.001 TRP S 47 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.21 ( 8861) covalent geometry : angle 0.58284 / 0.31 (12038) SS BOND : bond 0.00308 / 0.16 ( 4) SS BOND : angle 0.67047 / 0.39 ( 8) hydrogen bonds : bond 0.04428 / 3.02 ( 404) hydrogen bonds : angle 4.26808 / 2.94 ( 1131) link_NAG-ASN : bond 0.00047 / 0.02 ( 1) link_NAG-ASN : angle 1.72538 / 0.97 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.261 Fit side-chains REVERT: A 53 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7278 (mtp) REVERT: B 137 ARG cc_start: 0.8066 (tpt90) cc_final: 0.7476 (tpp-160) REVERT: B 234 PHE cc_start: 0.8981 (OUTLIER) cc_final: 0.8633 (m-80) REVERT: C 42 GLU cc_start: 0.7330 (mp0) cc_final: 0.6568 (mp0) REVERT: R 217 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7405 (tt0) outliers start: 33 outliers final: 19 residues processed: 156 average time/residue: 0.0834 time to fit residues: 17.8425 Evaluate side-chains 147 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 217 GLN Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 268 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 81 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 30.0000 chunk 76 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 322 HIS ** S 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.151118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.116844 restraints weight = 11450.508| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.51 r_work: 0.3314 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8866 Z= 0.189 Angle : 0.582 9.529 12049 Z= 0.299 Chirality : 0.043 0.168 1378 Planarity : 0.004 0.046 1522 Dihedral : 4.440 17.974 1235 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.57 % Allowed : 25.86 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.25), residues: 1115 helix: 1.88 (0.28), residues: 360 sheet: 0.10 (0.31), residues: 268 loop : -1.08 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 270 TYR 0.028 0.002 TYR S 235 PHE 0.026 0.002 PHE R 38 TRP 0.008 0.001 TRP S 47 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 ( 8861) covalent geometry : angle 0.58103 / 0.30 (12038) SS BOND : bond 0.00278 / 0.15 ( 4) SS BOND : angle 0.59254 / 0.34 ( 8) hydrogen bonds : bond 0.04203 / 2.86 ( 404) hydrogen bonds : angle 4.19194 / 2.89 ( 1131) link_NAG-ASN : bond 0.00004 / 0.00 ( 1) link_NAG-ASN : angle 1.78306 / 1.00 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.305 Fit side-chains REVERT: A 53 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7345 (mtp) REVERT: A 197 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8533 (mtmt) REVERT: S 13 GLN cc_start: 0.7907 (pm20) cc_final: 0.7539 (pp30) REVERT: B 234 PHE cc_start: 0.9020 (OUTLIER) cc_final: 0.8664 (m-80) REVERT: C 42 GLU cc_start: 0.7522 (mp0) cc_final: 0.6726 (mp0) REVERT: R 190 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6842 (mm-30) REVERT: R 217 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7523 (tt0) outliers start: 32 outliers final: 20 residues processed: 149 average time/residue: 0.0758 time to fit residues: 15.6579 Evaluate side-chains 144 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 190 GLU Chi-restraints excluded: chain R residue 217 GLN Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 268 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 322 HIS ** S 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.152152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.117719 restraints weight = 11299.214| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.51 r_work: 0.3340 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8866 Z= 0.141 Angle : 0.553 11.187 12049 Z= 0.282 Chirality : 0.042 0.170 1378 Planarity : 0.004 0.047 1522 Dihedral : 4.238 17.323 1235 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.46 % Allowed : 26.42 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.26), residues: 1115 helix: 1.99 (0.28), residues: 360 sheet: 0.16 (0.32), residues: 268 loop : -1.03 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 180 TYR 0.024 0.001 TYR S 235 PHE 0.026 0.001 PHE R 38 TRP 0.008 0.001 TRP S 47 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 8861) covalent geometry : angle 0.55274 / 0.28 (12038) SS BOND : bond 0.00254 / 0.13 ( 4) SS BOND : angle 0.50229 / 0.29 ( 8) hydrogen bonds : bond 0.03839 / 2.62 ( 404) hydrogen bonds : angle 4.09263 / 2.82 ( 1131) link_NAG-ASN : bond 0.00038 / 0.02 ( 1) link_NAG-ASN : angle 1.75034 / 0.98 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.255 Fit side-chains REVERT: S 13 GLN cc_start: 0.7906 (pm20) cc_final: 0.7597 (pp30) REVERT: B 234 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.8652 (m-80) REVERT: C 42 GLU cc_start: 0.7484 (mp0) cc_final: 0.6628 (mp0) REVERT: R 165 LYS cc_start: 0.7099 (mmtt) cc_final: 0.6344 (mttt) REVERT: R 190 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6734 (mm-30) REVERT: R 217 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7528 (tt0) outliers start: 31 outliers final: 20 residues processed: 146 average time/residue: 0.0878 time to fit residues: 17.4064 Evaluate side-chains 144 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 190 GLU Chi-restraints excluded: chain R residue 217 GLN Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 268 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 69 optimal weight: 4.9990 chunk 76 optimal weight: 40.0000 chunk 13 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 44 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 HIS ** S 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.150723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.116615 restraints weight = 11411.298| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.49 r_work: 0.3311 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8866 Z= 0.200 Angle : 0.593 10.040 12049 Z= 0.305 Chirality : 0.044 0.189 1378 Planarity : 0.004 0.049 1522 Dihedral : 4.496 18.059 1235 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.68 % Allowed : 26.20 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.25), residues: 1115 helix: 1.85 (0.28), residues: 361 sheet: 0.09 (0.31), residues: 268 loop : -1.09 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 27 TYR 0.026 0.002 TYR S 235 PHE 0.027 0.002 PHE R 38 TRP 0.008 0.001 TRP S 47 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.20 ( 8861) covalent geometry : angle 0.59218 / 0.30 (12038) SS BOND : bond 0.00273 / 0.14 ( 4) SS BOND : angle 0.59010 / 0.34 ( 8) hydrogen bonds : bond 0.04208 / 2.85 ( 404) hydrogen bonds : angle 4.18051 / 2.88 ( 1131) link_NAG-ASN : bond 0.00029 / 0.02 ( 1) link_NAG-ASN : angle 1.78947 / 1.00 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 0.216 Fit side-chains REVERT: A 53 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7333 (mtp) REVERT: S 13 GLN cc_start: 0.7876 (pm20) cc_final: 0.7611 (pp30) REVERT: B 234 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8674 (m-80) REVERT: C 42 GLU cc_start: 0.7446 (mp0) cc_final: 0.6540 (mp0) REVERT: R 165 LYS cc_start: 0.7196 (mmtt) cc_final: 0.6485 (mttt) REVERT: R 190 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6765 (mm-30) REVERT: R 217 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7515 (tt0) outliers start: 33 outliers final: 25 residues processed: 149 average time/residue: 0.0772 time to fit residues: 16.1458 Evaluate side-chains 149 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 190 GLU Chi-restraints excluded: chain R residue 217 GLN Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 268 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 50 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 HIS S 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.150234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.116740 restraints weight = 11157.380| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.42 r_work: 0.3351 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8866 Z= 0.122 Angle : 0.555 10.787 12049 Z= 0.282 Chirality : 0.042 0.137 1378 Planarity : 0.004 0.042 1522 Dihedral : 4.213 20.303 1235 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.23 % Allowed : 27.09 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.26), residues: 1115 helix: 2.11 (0.28), residues: 360 sheet: 0.19 (0.32), residues: 268 loop : -1.04 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 27 TYR 0.033 0.001 TYR S 235 PHE 0.027 0.001 PHE R 38 TRP 0.008 0.001 TRP R 188 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 8861) covalent geometry : angle 0.55487 / 0.28 (12038) SS BOND : bond 0.00220 / 0.11 ( 4) SS BOND : angle 0.47721 / 0.28 ( 8) hydrogen bonds : bond 0.03664 / 2.49 ( 404) hydrogen bonds : angle 4.07149 / 2.80 ( 1131) link_NAG-ASN : bond 0.00057 / 0.03 ( 1) link_NAG-ASN : angle 1.71353 / 0.96 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.414 Fit side-chains REVERT: S 13 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7682 (pp30) REVERT: B 234 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.8612 (m-80) REVERT: C 42 GLU cc_start: 0.7435 (mp0) cc_final: 0.6541 (mp0) REVERT: R 165 LYS cc_start: 0.7228 (mmtt) cc_final: 0.6526 (mttt) REVERT: R 190 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6790 (mm-30) REVERT: R 217 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7598 (tt0) outliers start: 29 outliers final: 22 residues processed: 139 average time/residue: 0.0830 time to fit residues: 16.2678 Evaluate side-chains 146 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain S residue 13 GLN Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 190 GLU Chi-restraints excluded: chain R residue 217 GLN Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 268 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 51 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.150292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.116852 restraints weight = 11108.064| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.42 r_work: 0.3357 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.175 8866 Z= 0.236 Angle : 0.919 59.058 12049 Z= 0.521 Chirality : 0.043 0.424 1378 Planarity : 0.004 0.044 1522 Dihedral : 4.207 19.820 1235 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.12 % Allowed : 27.20 % Favored : 69.68 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.26), residues: 1115 helix: 2.12 (0.28), residues: 360 sheet: 0.19 (0.32), residues: 268 loop : -1.06 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 27 TYR 0.031 0.001 TYR S 235 PHE 0.025 0.001 PHE R 232 TRP 0.008 0.001 TRP R 188 HIS 0.002 0.000 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.24 ( 8861) covalent geometry : angle 0.91897 / 0.52 (12038) SS BOND : bond 0.00221 / 0.11 ( 4) SS BOND : angle 0.47386 / 0.27 ( 8) hydrogen bonds : bond 0.03657 / 2.49 ( 404) hydrogen bonds : angle 4.07050 / 2.80 ( 1131) link_NAG-ASN : bond 0.00058 / 0.03 ( 1) link_NAG-ASN : angle 1.71291 / 0.96 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2105.42 seconds wall clock time: 36 minutes 42.85 seconds (2202.85 seconds total)