Starting phenix.real_space_refine on Thu Aug 6 10:02:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ee8_47951/08_2026/9ee8_47951.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ee8_47951/08_2026/9ee8_47951.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ee8_47951/08_2026/9ee8_47951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ee8_47951/08_2026/9ee8_47951.map" model { file = "/net/cci-nas-00/data/ceres_data/9ee8_47951/08_2026/9ee8_47951.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ee8_47951/08_2026/9ee8_47951.cif" } resolution = 2.63 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= 0.011 sd= 0.383 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 53 5.16 5 C 4877 2.51 5 N 1327 2.21 5 O 1394 1.98 5 H 7180 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14831 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 4195 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 9, 'TRANS': 268} Chain breaks: 2 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 4724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 4724 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 4, 'GLN:plan1': 6, 'ARG:plan': 7, 'GLU:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 93 Chain: "C" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 594 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "D" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3460 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'GLU:plan': 7, 'ASP:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 87 Chain: "E" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1839 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'ADN%rna3p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 2.72, per 1000 atoms: 0.18 Number of scatterers: 14831 At special positions: 0 Unit cell: (73.48, 100.2, 128.59, 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 53 16.00 O 1394 8.00 N 1327 7.00 C 4877 6.00 H 7180 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 146 " distance=2.03 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 166 " distance=2.06 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 262 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 107 " 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 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 481.2 milliseconds 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1926 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 42.6% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 8 through 34 removed outlier: 4.007A pdb=" N GLY A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL A 27 " --> pdb=" O GLY A 23 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS A 28 " --> pdb=" O ASN A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 69 removed outlier: 3.894A pdb=" N PHE A 44 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILE A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) Proline residue: A 61 - end of helix removed outlier: 3.632A pdb=" N GLY A 69 " --> pdb=" O THR A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 108 removed outlier: 3.982A pdb=" N SER A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 116 Processing helix chain 'A' and resid 117 through 137 Processing helix chain 'A' and resid 138 through 143 removed outlier: 3.885A pdb=" N GLY A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 138 through 143' Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 173 through 180 Processing helix chain 'A' and resid 180 through 186 Processing helix chain 'A' and resid 186 through 209 Processing helix chain 'A' and resid 224 through 259 removed outlier: 4.069A pdb=" N ILE A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Proline residue: A 248 - end of helix Processing helix chain 'A' and resid 266 through 279 Processing helix chain 'A' and resid 279 through 289 Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 292 through 307 Processing helix chain 'B' and resid 6 through 26 removed outlier: 3.756A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 12 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 12 through 40 removed outlier: 4.041A pdb=" N GLU D 16 " --> pdb=" O GLN D 12 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS D 32 " --> pdb=" O LYS D 28 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR D 40 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 56 removed outlier: 3.894A pdb=" N ILE D 56 " --> pdb=" O LYS D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 252 through 269 removed outlier: 4.452A pdb=" N GLN D 257 " --> pdb=" O TYR D 253 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLU D 258 " --> pdb=" O ASN D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 294 Processing helix chain 'D' and resid 297 through 301 Processing helix chain 'D' and resid 302 through 308 Processing helix chain 'D' and resid 321 through 342 removed outlier: 3.527A pdb=" N PHE D 335 " --> pdb=" O ILE D 331 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE D 338 " --> pdb=" O GLU D 334 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER D 342 " --> pdb=" O ILE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 381 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.541A pdb=" N THR E 91 " --> pdb=" O PRO E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.541A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.787A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.735A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.773A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.909A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.719A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.369A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 208 through 214 removed outlier: 3.597A pdb=" N PHE D 212 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS D 41 " --> pdb=" O ASN D 218 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ARG D 42 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ILE D 245 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU D 44 " --> pdb=" O ILE D 245 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N VAL D 247 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU D 46 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N ASP D 249 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE D 244 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N PHE D 280 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE D 246 " --> pdb=" O PHE D 280 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN D 282 " --> pdb=" O PHE D 246 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL D 248 " --> pdb=" O ASN D 282 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 8 removed outlier: 3.612A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.064A pdb=" N GLY E 10 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1128 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: 3.26 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 7154 1.04 - 1.24: 921 1.24 - 1.44: 2524 1.44 - 1.63: 4324 1.63 - 1.83: 71 Bond restraints: 14994 Sorted by residual: bond pdb=" CA PHE A 168 " pdb=" C PHE A 168 " ideal model delta sigma weight residual 1.524 1.415 0.109 1.26e-02 6.30e+03 7.50e+01 bond pdb=" CA PHE D 238 " pdb=" C PHE D 238 " ideal model delta sigma weight residual 1.530 1.457 0.074 1.23e-02 6.61e+03 3.61e+01 bond pdb=" C PHE D 238 " pdb=" O PHE D 238 " ideal model delta sigma weight residual 1.228 1.159 0.069 1.39e-02 5.18e+03 2.46e+01 bond pdb=" C ILE A 237 " pdb=" N ILE A 238 " ideal model delta sigma weight residual 1.333 1.276 0.058 1.22e-02 6.72e+03 2.24e+01 bond pdb=" CA THR D 315 " pdb=" C THR D 315 " ideal model delta sigma weight residual 1.524 1.469 0.055 1.21e-02 6.83e+03 2.10e+01 ... (remaining 14989 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 26678 2.19 - 4.37: 165 4.37 - 6.56: 26 6.56 - 8.75: 2 8.75 - 10.93: 4 Bond angle restraints: 26875 Sorted by residual: angle pdb=" N PHE A 83 " pdb=" CA PHE A 83 " pdb=" C PHE A 83 " ideal model delta sigma weight residual 112.90 104.39 8.51 1.31e+00 5.83e-01 4.22e+01 angle pdb=" C PHE A 168 " pdb=" CA PHE A 168 " pdb=" CB PHE A 168 " ideal model delta sigma weight residual 110.90 100.96 9.94 1.58e+00 4.01e-01 3.96e+01 angle pdb=" C GLU D 317 " pdb=" CA GLU D 317 " pdb=" CB GLU D 317 " ideal model delta sigma weight residual 109.42 119.00 -9.58 1.57e+00 4.06e-01 3.72e+01 angle pdb=" C GLU D 317 " pdb=" N PRO D 318 " pdb=" CA PRO D 318 " ideal model delta sigma weight residual 119.98 126.46 -6.48 1.16e+00 7.43e-01 3.12e+01 angle pdb=" C GLU A 169 " pdb=" N ASP A 170 " pdb=" CA ASP A 170 " ideal model delta sigma weight residual 120.68 111.20 9.48 1.70e+00 3.46e-01 3.11e+01 ... (remaining 26870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 6399 17.23 - 34.46: 546 34.46 - 51.68: 183 51.68 - 68.91: 54 68.91 - 86.14: 10 Dihedral angle restraints: 7192 sinusoidal: 3666 harmonic: 3526 Sorted by residual: dihedral pdb=" CB CYS A 259 " pdb=" SG CYS A 259 " pdb=" SG CYS A 262 " pdb=" CB CYS A 262 " ideal model delta sinusoidal sigma weight residual 93.00 165.03 -72.03 1 1.00e+01 1.00e-02 6.64e+01 dihedral pdb=" CB CYS A 74 " pdb=" SG CYS A 74 " pdb=" SG CYS A 146 " pdb=" CB CYS A 146 " ideal model delta sinusoidal sigma weight residual 93.00 156.56 -63.56 1 1.00e+01 1.00e-02 5.33e+01 dihedral pdb=" C PHE A 168 " pdb=" N PHE A 168 " pdb=" CA PHE A 168 " pdb=" CB PHE A 168 " ideal model delta harmonic sigma weight residual -122.60 -111.29 -11.31 0 2.50e+00 1.60e-01 2.05e+01 ... (remaining 7189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 867 0.035 - 0.070: 254 0.070 - 0.104: 77 0.104 - 0.139: 45 0.139 - 0.174: 3 Chirality restraints: 1246 Sorted by residual: chirality pdb=" CA VAL A 164 " pdb=" N VAL A 164 " pdb=" C VAL A 164 " pdb=" CB VAL A 164 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.17 2.00e-01 2.50e+01 7.58e-01 chirality pdb=" CA PRO D 316 " pdb=" N PRO D 316 " pdb=" C PRO D 316 " pdb=" CB PRO D 316 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CA ALA A 236 " pdb=" N ALA A 236 " pdb=" C ALA A 236 " pdb=" CB ALA A 236 " both_signs ideal model delta sigma weight residual False 2.48 2.32 0.17 2.00e-01 2.50e+01 6.99e-01 ... (remaining 1243 not shown) Planarity restraints: 2341 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 239 " -0.105 2.00e-02 2.50e+03 1.16e-01 2.02e+02 pdb=" CG ASN D 239 " -0.005 2.00e-02 2.50e+03 pdb=" OD1 ASN D 239 " 0.111 2.00e-02 2.50e+03 pdb=" ND2 ASN D 239 " -0.005 2.00e-02 2.50e+03 pdb="HD21 ASN D 239 " 0.171 2.00e-02 2.50e+03 pdb="HD22 ASN D 239 " -0.167 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 166 " -0.023 2.00e-02 2.50e+03 4.66e-02 2.17e+01 pdb=" C CYS A 166 " 0.081 2.00e-02 2.50e+03 pdb=" O CYS A 166 " -0.030 2.00e-02 2.50e+03 pdb=" N LEU A 167 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 235 " 0.023 2.00e-02 2.50e+03 4.53e-02 2.05e+01 pdb=" C LEU A 235 " -0.078 2.00e-02 2.50e+03 pdb=" O LEU A 235 " 0.029 2.00e-02 2.50e+03 pdb=" N ALA A 236 " 0.027 2.00e-02 2.50e+03 ... (remaining 2338 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 1244 2.22 - 2.82: 30864 2.82 - 3.41: 37802 3.41 - 4.01: 51612 4.01 - 4.60: 79417 Nonbonded interactions: 200939 Sorted by model distance: nonbonded pdb=" O ARG E 98 " pdb=" HH TYR E 115 " model vdw 1.631 2.450 nonbonded pdb=" O ALA A 59 " pdb=" H ALA A 63 " model vdw 1.647 2.450 nonbonded pdb=" OD2 ASP D 229 " pdb=" H SER E 112 " model vdw 1.662 2.450 nonbonded pdb=" O ILE D 56 " pdb="HD21 ASN D 361 " model vdw 1.667 2.450 nonbonded pdb=" O TYR B 145 " pdb=" H GLY B 162 " model vdw 1.685 2.450 ... (remaining 200934 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: 2.290 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: 0.100 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.960 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: 0.010 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 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 : 0.005 0.109 7820 Z= 0.294 Angle : 0.607 9.945 10667 Z= 0.369 Chirality : 0.041 0.174 1246 Planarity : 0.005 0.063 1357 Dihedral : 16.076 86.139 2650 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.26 % Allowed : 25.13 % Favored : 74.60 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.28), residues: 1009 helix: 2.52 (0.28), residues: 389 sheet: 0.35 (0.37), residues: 214 loop : -0.56 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 38 TYR 0.021 0.001 TYR A 9 PHE 0.024 0.001 PHE D 238 TRP 0.006 0.001 TRP D 234 HIS 0.002 0.000 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.29 ( 7814) covalent geometry : angle 0.60525 / 0.37 (10655) SS BOND : bond 0.01232 / 0.73 ( 6) SS BOND : angle 1.59233 / 0.98 ( 12) hydrogen bonds : bond 0.15796 / 10.87 ( 398) hydrogen bonds : angle 6.12118 / 4.41 ( 1128) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 6 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 307 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 211 MET cc_start: 0.7245 (mtp) cc_final: 0.6985 (mtp) REVERT: A 234 SER cc_start: 0.9451 (t) cc_final: 0.9236 (p) REVERT: D 16 GLU cc_start: 0.8507 (mp0) cc_final: 0.8069 (mp0) REVERT: D 27 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8137 (mm-30) REVERT: D 208 PHE cc_start: 0.8121 (m-80) cc_final: 0.7764 (m-80) REVERT: D 270 ARG cc_start: 0.8818 (ttt-90) cc_final: 0.8612 (tpt-90) outliers start: 2 outliers final: 0 residues processed: 146 average time/residue: 1.1748 time to fit residues: 181.8952 Evaluate side-chains 106 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.0050 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 259 GLN C 18 GLN D 284 GLN D 380 GLN E 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.091895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.075598 restraints weight = 44630.848| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.86 r_work: 0.2943 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7820 Z= 0.124 Angle : 0.498 5.235 10667 Z= 0.269 Chirality : 0.040 0.148 1246 Planarity : 0.004 0.050 1357 Dihedral : 4.484 38.298 1122 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.25 % Allowed : 25.66 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.28), residues: 1009 helix: 2.66 (0.28), residues: 391 sheet: 0.57 (0.36), residues: 210 loop : -0.49 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 111 TYR 0.008 0.001 TYR D 329 PHE 0.012 0.001 PHE A 83 TRP 0.009 0.001 TRP D 234 HIS 0.002 0.000 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 7814) covalent geometry : angle 0.49667 / 0.27 (10655) SS BOND : bond 0.00533 / 0.38 ( 6) SS BOND : angle 1.25047 / 0.77 ( 12) hydrogen bonds : bond 0.04144 / 2.78 ( 398) hydrogen bonds : angle 4.53176 / 3.24 ( 1128) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 6 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 307 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 MET cc_start: 0.7343 (mtp) cc_final: 0.7087 (mtp) REVERT: A 234 SER cc_start: 0.9505 (t) cc_final: 0.9276 (p) REVERT: B 234 PHE cc_start: 0.9217 (OUTLIER) cc_final: 0.8492 (t80) REVERT: C 36 ASP cc_start: 0.8966 (m-30) cc_final: 0.8712 (m-30) REVERT: D 16 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8193 (mp0) REVERT: D 27 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8430 (mm-30) REVERT: D 382 GLU cc_start: 0.8997 (tp30) cc_final: 0.8587 (mp0) REVERT: E 18 LEU cc_start: 0.8175 (tp) cc_final: 0.7952 (mp) outliers start: 17 outliers final: 7 residues processed: 136 average time/residue: 1.0461 time to fit residues: 151.7166 Evaluate side-chains 120 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 239 ASN Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 11 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 69 optimal weight: 0.0270 chunk 14 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.4644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 18 GLN D 284 GLN E 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.091286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.075112 restraints weight = 44628.332| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.86 r_work: 0.2937 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7820 Z= 0.155 Angle : 0.488 5.883 10667 Z= 0.265 Chirality : 0.040 0.140 1246 Planarity : 0.004 0.074 1357 Dihedral : 4.310 32.443 1122 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.25 % Allowed : 24.34 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.28), residues: 1009 helix: 2.57 (0.27), residues: 391 sheet: 0.49 (0.35), residues: 217 loop : -0.45 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 206 TYR 0.010 0.001 TYR D 329 PHE 0.012 0.001 PHE E 108 TRP 0.009 0.001 TRP D 234 HIS 0.002 0.001 HIS A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 7814) covalent geometry : angle 0.48637 / 0.26 (10655) SS BOND : bond 0.00728 / 0.51 ( 6) SS BOND : angle 1.42023 / 0.87 ( 12) hydrogen bonds : bond 0.03946 / 2.63 ( 398) hydrogen bonds : angle 4.39988 / 3.15 ( 1128) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 6 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 307 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.303 Fit side-chains REVERT: A 143 TRP cc_start: 0.8299 (t60) cc_final: 0.7413 (t60) REVERT: A 211 MET cc_start: 0.7403 (mtp) cc_final: 0.7148 (mtp) REVERT: A 234 SER cc_start: 0.9505 (t) cc_final: 0.9295 (p) REVERT: A 237 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8646 (mt) REVERT: B 87 THR cc_start: 0.8774 (m) cc_final: 0.8565 (p) REVERT: B 234 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.8511 (t80) REVERT: D 16 GLU cc_start: 0.8633 (mp0) cc_final: 0.8222 (mp0) REVERT: D 27 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8404 (mm-30) REVERT: D 382 GLU cc_start: 0.8970 (tp30) cc_final: 0.8608 (mp0) outliers start: 17 outliers final: 7 residues processed: 127 average time/residue: 0.8796 time to fit residues: 119.0330 Evaluate side-chains 113 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 49 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 7 optimal weight: 1.9990 chunk 89 optimal weight: 0.0370 chunk 59 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 18 GLN E 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.090469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.074540 restraints weight = 44556.644| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.82 r_work: 0.2936 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7820 Z= 0.141 Angle : 0.480 5.197 10667 Z= 0.259 Chirality : 0.040 0.139 1246 Planarity : 0.004 0.070 1357 Dihedral : 4.262 32.246 1122 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.98 % Allowed : 25.00 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.28), residues: 1009 helix: 2.58 (0.27), residues: 391 sheet: 0.55 (0.35), residues: 215 loop : -0.49 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 270 TYR 0.009 0.001 TYR D 329 PHE 0.011 0.001 PHE E 108 TRP 0.009 0.001 TRP D 234 HIS 0.002 0.000 HIS A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 7814) covalent geometry : angle 0.47742 / 0.26 (10655) SS BOND : bond 0.00627 / 0.44 ( 6) SS BOND : angle 1.49938 / 0.87 ( 12) hydrogen bonds : bond 0.03668 / 2.45 ( 398) hydrogen bonds : angle 4.29819 / 3.08 ( 1128) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 6 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 307 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.427 Fit side-chains REVERT: A 143 TRP cc_start: 0.8281 (t60) cc_final: 0.7367 (t60) REVERT: A 211 MET cc_start: 0.7364 (mtp) cc_final: 0.7157 (mtp) REVERT: A 234 SER cc_start: 0.9505 (t) cc_final: 0.9280 (p) REVERT: A 237 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8668 (mt) REVERT: B 87 THR cc_start: 0.8762 (m) cc_final: 0.8550 (p) REVERT: B 234 PHE cc_start: 0.9269 (OUTLIER) cc_final: 0.8524 (t80) REVERT: D 16 GLU cc_start: 0.8632 (mp0) cc_final: 0.8208 (mp0) REVERT: D 27 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8414 (mt-10) REVERT: D 53 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8014 (ttmm) REVERT: D 382 GLU cc_start: 0.8978 (tp30) cc_final: 0.8618 (mp0) outliers start: 15 outliers final: 7 residues processed: 113 average time/residue: 1.1717 time to fit residues: 140.6409 Evaluate side-chains 113 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 11 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 0.0770 chunk 7 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.089322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.073272 restraints weight = 45105.220| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.83 r_work: 0.2913 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7820 Z= 0.180 Angle : 0.493 5.786 10667 Z= 0.267 Chirality : 0.040 0.137 1246 Planarity : 0.004 0.078 1357 Dihedral : 4.356 32.466 1122 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.12 % Allowed : 25.13 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.27), residues: 1009 helix: 2.53 (0.27), residues: 385 sheet: 0.47 (0.35), residues: 216 loop : -0.60 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 206 TYR 0.010 0.001 TYR D 329 PHE 0.015 0.001 PHE E 108 TRP 0.009 0.001 TRP D 234 HIS 0.002 0.001 HIS A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 ( 7814) covalent geometry : angle 0.49009 / 0.27 (10655) SS BOND : bond 0.00735 / 0.51 ( 6) SS BOND : angle 1.56671 / 0.95 ( 12) hydrogen bonds : bond 0.03886 / 2.59 ( 398) hydrogen bonds : angle 4.35193 / 3.12 ( 1128) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 6 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 307 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 143 TRP cc_start: 0.8298 (t60) cc_final: 0.7558 (t60) REVERT: A 234 SER cc_start: 0.9486 (t) cc_final: 0.9223 (p) REVERT: B 87 THR cc_start: 0.8764 (m) cc_final: 0.8559 (p) REVERT: B 259 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8271 (mt0) REVERT: D 16 GLU cc_start: 0.8613 (mp0) cc_final: 0.8148 (mp0) REVERT: D 382 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8621 (mp0) outliers start: 16 outliers final: 7 residues processed: 111 average time/residue: 1.1009 time to fit residues: 129.6763 Evaluate side-chains 107 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain E residue 49 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 99 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 98 optimal weight: 0.4980 chunk 89 optimal weight: 0.0570 chunk 31 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.091117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.075187 restraints weight = 44414.459| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.84 r_work: 0.2948 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7820 Z= 0.097 Angle : 0.462 4.271 10667 Z= 0.247 Chirality : 0.039 0.138 1246 Planarity : 0.004 0.077 1357 Dihedral : 4.083 29.132 1122 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.72 % Allowed : 24.87 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.28), residues: 1009 helix: 2.75 (0.27), residues: 385 sheet: 0.53 (0.35), residues: 215 loop : -0.52 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 206 TYR 0.008 0.001 TYR D 329 PHE 0.012 0.001 PHE D 222 TRP 0.008 0.001 TRP D 234 HIS 0.001 0.000 HIS A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 7814) covalent geometry : angle 0.46023 / 0.25 (10655) SS BOND : bond 0.00463 / 0.32 ( 6) SS BOND : angle 1.29266 / 0.77 ( 12) hydrogen bonds : bond 0.03310 / 2.20 ( 398) hydrogen bonds : angle 4.12620 / 2.95 ( 1128) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 6 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 307 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 9 TYR cc_start: 0.8325 (t80) cc_final: 0.8114 (t80) REVERT: A 143 TRP cc_start: 0.8291 (t60) cc_final: 0.7441 (t60) REVERT: A 234 SER cc_start: 0.9467 (t) cc_final: 0.9204 (p) REVERT: B 87 THR cc_start: 0.8741 (m) cc_final: 0.8534 (p) REVERT: B 259 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8188 (mt0) REVERT: D 16 GLU cc_start: 0.8617 (mp0) cc_final: 0.8169 (mp0) REVERT: D 53 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8128 (ttmm) REVERT: D 382 GLU cc_start: 0.8952 (tp30) cc_final: 0.8598 (mp0) outliers start: 13 outliers final: 5 residues processed: 118 average time/residue: 1.1262 time to fit residues: 141.5357 Evaluate side-chains 108 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain D residue 53 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 0.1980 chunk 41 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 18 GLN E 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.090365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.074350 restraints weight = 44592.439| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.83 r_work: 0.2933 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7820 Z= 0.133 Angle : 0.476 4.882 10667 Z= 0.255 Chirality : 0.040 0.134 1246 Planarity : 0.004 0.081 1357 Dihedral : 4.170 32.208 1122 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.98 % Allowed : 25.53 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.27), residues: 1009 helix: 2.74 (0.27), residues: 385 sheet: 0.53 (0.34), residues: 215 loop : -0.54 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 206 TYR 0.009 0.001 TYR D 329 PHE 0.013 0.001 PHE A 182 TRP 0.009 0.001 TRP D 234 HIS 0.001 0.000 HIS A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 7814) covalent geometry : angle 0.47405 / 0.25 (10655) SS BOND : bond 0.00606 / 0.42 ( 6) SS BOND : angle 1.39803 / 0.85 ( 12) hydrogen bonds : bond 0.03422 / 2.28 ( 398) hydrogen bonds : angle 4.15922 / 2.97 ( 1128) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 6 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 307 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 SER cc_start: 0.9463 (t) cc_final: 0.9195 (p) REVERT: B 87 THR cc_start: 0.8753 (m) cc_final: 0.8549 (p) REVERT: B 259 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8235 (mt0) REVERT: D 16 GLU cc_start: 0.8618 (mp0) cc_final: 0.8204 (mp0) REVERT: D 53 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8149 (ttmm) REVERT: D 382 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8587 (mp0) outliers start: 15 outliers final: 8 residues processed: 111 average time/residue: 1.1015 time to fit residues: 130.4681 Evaluate side-chains 109 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 382 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 40 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN C 18 GLN E 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.090596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.074948 restraints weight = 45168.520| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.86 r_work: 0.2918 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7820 Z= 0.134 Angle : 0.480 4.865 10667 Z= 0.257 Chirality : 0.040 0.135 1246 Planarity : 0.004 0.086 1357 Dihedral : 4.174 31.643 1122 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.12 % Allowed : 25.66 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.27), residues: 1009 helix: 2.76 (0.27), residues: 385 sheet: 0.56 (0.34), residues: 215 loop : -0.52 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 206 TYR 0.009 0.001 TYR D 329 PHE 0.015 0.001 PHE A 182 TRP 0.008 0.001 TRP D 234 HIS 0.002 0.000 HIS A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 7814) covalent geometry : angle 0.47786 / 0.26 (10655) SS BOND : bond 0.00618 / 0.43 ( 6) SS BOND : angle 1.42982 / 0.86 ( 12) hydrogen bonds : bond 0.03440 / 2.29 ( 398) hydrogen bonds : angle 4.16009 / 2.97 ( 1128) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 6 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 307 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 SER cc_start: 0.9456 (t) cc_final: 0.9183 (p) REVERT: A 302 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8364 (mm) REVERT: B 87 THR cc_start: 0.8760 (m) cc_final: 0.8551 (p) REVERT: B 172 GLU cc_start: 0.9177 (tp30) cc_final: 0.8968 (tp30) REVERT: B 259 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8224 (mt0) REVERT: D 16 GLU cc_start: 0.8582 (mp0) cc_final: 0.8138 (mp0) REVERT: D 53 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8136 (ttmm) REVERT: D 382 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8554 (mp0) outliers start: 16 outliers final: 8 residues processed: 112 average time/residue: 0.9915 time to fit residues: 118.5826 Evaluate side-chains 110 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain E residue 49 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 89 optimal weight: 0.0970 chunk 80 optimal weight: 0.1980 chunk 28 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN C 18 GLN E 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.092083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.076205 restraints weight = 44838.575| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.87 r_work: 0.2953 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7820 Z= 0.091 Angle : 0.463 4.568 10667 Z= 0.246 Chirality : 0.039 0.136 1246 Planarity : 0.004 0.078 1357 Dihedral : 3.997 29.885 1122 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.46 % Allowed : 26.06 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.28), residues: 1009 helix: 2.92 (0.27), residues: 385 sheet: 0.56 (0.34), residues: 215 loop : -0.45 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 206 TYR 0.008 0.001 TYR D 329 PHE 0.014 0.001 PHE A 182 TRP 0.009 0.001 TRP B 297 HIS 0.002 0.000 HIS D 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 ( 7814) covalent geometry : angle 0.46125 / 0.25 (10655) SS BOND : bond 0.00386 / 0.27 ( 6) SS BOND : angle 1.17529 / 0.71 ( 12) hydrogen bonds : bond 0.03087 / 2.04 ( 398) hydrogen bonds : angle 4.04531 / 2.89 ( 1128) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 6 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 307 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 TRP cc_start: 0.8348 (t60) cc_final: 0.7868 (t60) REVERT: A 234 SER cc_start: 0.9437 (t) cc_final: 0.9166 (p) REVERT: B 259 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8188 (mt0) REVERT: D 16 GLU cc_start: 0.8591 (mp0) cc_final: 0.8159 (mp0) REVERT: D 53 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8129 (ttmm) REVERT: D 382 GLU cc_start: 0.8900 (tp30) cc_final: 0.8525 (mp0) outliers start: 11 outliers final: 7 residues processed: 120 average time/residue: 0.8922 time to fit residues: 114.2858 Evaluate side-chains 116 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain D residue 53 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 27 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN A 181 ASN A 284 ASN C 18 GLN E 77 ASN E 120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.090076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.074468 restraints weight = 45144.035| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.84 r_work: 0.2920 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7820 Z= 0.175 Angle : 0.506 5.653 10667 Z= 0.272 Chirality : 0.040 0.138 1246 Planarity : 0.004 0.079 1357 Dihedral : 4.256 32.777 1122 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.85 % Allowed : 26.46 % Favored : 71.69 % 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: 1.45 (0.27), residues: 1009 helix: 2.71 (0.27), residues: 385 sheet: 0.53 (0.34), residues: 216 loop : -0.52 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 206 TYR 0.011 0.001 TYR D 329 PHE 0.017 0.001 PHE A 182 TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 7814) covalent geometry : angle 0.50297 / 0.27 (10655) SS BOND : bond 0.00773 / 0.54 ( 6) SS BOND : angle 1.61844 / 0.99 ( 12) hydrogen bonds : bond 0.03623 / 2.41 ( 398) hydrogen bonds : angle 4.24249 / 3.03 ( 1128) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 6 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 307 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 SER cc_start: 0.9445 (t) cc_final: 0.9171 (p) REVERT: A 302 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8375 (mm) REVERT: B 259 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8221 (mt0) REVERT: D 16 GLU cc_start: 0.8569 (mp0) cc_final: 0.8123 (mp0) REVERT: D 53 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8150 (ttmm) REVERT: D 382 GLU cc_start: 0.8919 (tp30) cc_final: 0.8507 (mp0) outliers start: 14 outliers final: 9 residues processed: 112 average time/residue: 0.9990 time to fit residues: 118.9132 Evaluate side-chains 109 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain E residue 49 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 6 optimal weight: 1.9990 chunk 44 optimal weight: 0.0370 chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 0.0980 chunk 91 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN A 284 ASN C 18 GLN E 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.090429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.074520 restraints weight = 44696.754| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.84 r_work: 0.2946 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7820 Z= 0.101 Angle : 0.473 5.006 10667 Z= 0.252 Chirality : 0.039 0.135 1246 Planarity : 0.004 0.076 1357 Dihedral : 4.068 31.065 1122 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.72 % Allowed : 26.32 % Favored : 71.96 % 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 are not related in a simple way. whole: 1.62 (0.27), residues: 1009 helix: 2.87 (0.27), residues: 385 sheet: 0.64 (0.34), residues: 213 loop : -0.44 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 206 TYR 0.007 0.001 TYR D 329 PHE 0.015 0.001 PHE A 182 TRP 0.008 0.001 TRP D 234 HIS 0.002 0.000 HIS D 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 7814) covalent geometry : angle 0.47114 / 0.25 (10655) SS BOND : bond 0.00464 / 0.32 ( 6) SS BOND : angle 1.25084 / 0.75 ( 12) hydrogen bonds : bond 0.03189 / 2.12 ( 398) hydrogen bonds : angle 4.07746 / 2.91 ( 1128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5487.28 seconds wall clock time: 93 minutes 23.32 seconds (5603.32 seconds total)