Starting phenix.real_space_refine on Fri May 16 17:43:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ee8_47951/05_2025/9ee8_47951.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ee8_47951/05_2025/9ee8_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_47951/05_2025/9ee8_47951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ee8_47951/05_2025/9ee8_47951.map" model { file = "/net/cci-nas-00/data/ceres_data/9ee8_47951/05_2025/9ee8_47951.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ee8_47951/05_2025/9ee8_47951.cif" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'PHE:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, '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: {'GLN:plan1': 6, 'GLU:plan': 4, 'ARG:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 4} 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: {'GLU:plan': 5, 'ARG:plan': 2, '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, 'GLU:plan': 7, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 6} 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: 8.04, per 1000 atoms: 0.54 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: 3.56 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.28 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: 5.19 Time building geometry restraints manager: 4.19 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: 2.770 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: 0.270 Extract box with map and model: 0.560 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 33.960 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.001 TRP D 234 HIS 0.002 0.000 HIS A 250 PHE 0.024 0.001 PHE D 238 TYR 0.021 0.001 TYR A 9 ARG 0.009 0.000 ARG D 38 Details of bonding type rmsd hydrogen bonds : bond 0.15796 ( 398) hydrogen bonds : angle 6.12118 ( 1128) SS BOND : bond 0.01232 ( 6) SS BOND : angle 1.59233 ( 12) covalent geometry : bond 0.00453 ( 7814) covalent geometry : angle 0.60525 (10655) *********************** 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 : 1.081 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: 0.7763 (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: 2.5477 time to fit residues: 392.6491 Evaluate side-chains 103 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 0.0970 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3318 r_free = 0.3318 target = 0.091444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.075463 restraints weight = 44426.248| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.84 r_work: 0.2924 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7820 Z= 0.174 Angle : 0.522 6.096 10667 Z= 0.283 Chirality : 0.041 0.146 1246 Planarity : 0.005 0.055 1357 Dihedral : 4.615 38.593 1122 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.51 % Allowed : 24.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.28), residues: 1009 helix: 2.53 (0.27), residues: 392 sheet: 0.49 (0.36), residues: 212 loop : -0.53 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 234 HIS 0.002 0.000 HIS A 230 PHE 0.013 0.001 PHE E 108 TYR 0.010 0.001 TYR D 329 ARG 0.006 0.001 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.04272 ( 398) hydrogen bonds : angle 4.59971 ( 1128) SS BOND : bond 0.00736 ( 6) SS BOND : angle 1.51338 ( 12) covalent geometry : bond 0.00386 ( 7814) covalent geometry : angle 0.52017 (10655) *********************** 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 136 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 1.193 Fit side-chains revert: symmetry clash REVERT: A 107 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7853 (tmt-80) REVERT: A 211 MET cc_start: 0.7383 (mtp) cc_final: 0.7109 (mtp) REVERT: A 234 SER cc_start: 0.9506 (t) cc_final: 0.9271 (p) REVERT: B 234 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.8480 (t80) REVERT: C 36 ASP cc_start: 0.8968 (m-30) cc_final: 0.8740 (m-30) REVERT: D 16 GLU cc_start: 0.8643 (mp0) cc_final: 0.8233 (mp0) REVERT: D 382 GLU cc_start: 0.9000 (tp30) cc_final: 0.8574 (mp0) outliers start: 19 outliers final: 7 residues processed: 130 average time/residue: 2.4697 time to fit residues: 340.0811 Evaluate side-chains 114 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain D residue 239 ASN 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 95 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3267 r_free = 0.3267 target = 0.088122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.072206 restraints weight = 45292.851| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.86 r_work: 0.2884 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7820 Z= 0.232 Angle : 0.534 7.061 10667 Z= 0.292 Chirality : 0.041 0.145 1246 Planarity : 0.005 0.079 1357 Dihedral : 4.669 35.024 1122 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.31 % Allowed : 23.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.27), residues: 1009 helix: 2.28 (0.27), residues: 391 sheet: 0.37 (0.35), residues: 218 loop : -0.61 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 234 HIS 0.003 0.001 HIS A 230 PHE 0.018 0.001 PHE E 108 TYR 0.011 0.002 TYR A 197 ARG 0.007 0.000 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.04530 ( 398) hydrogen bonds : angle 4.62833 ( 1128) SS BOND : bond 0.00979 ( 6) SS BOND : angle 1.99383 ( 12) covalent geometry : bond 0.00523 ( 7814) covalent geometry : angle 0.53050 (10655) *********************** 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 130 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 1.227 Fit side-chains REVERT: A 107 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7828 (tmt-80) REVERT: A 234 SER cc_start: 0.9479 (t) cc_final: 0.9269 (p) REVERT: A 237 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8686 (mt) REVERT: B 87 THR cc_start: 0.8806 (m) cc_final: 0.8605 (p) REVERT: B 234 PHE cc_start: 0.9316 (OUTLIER) cc_final: 0.8563 (t80) REVERT: D 16 GLU cc_start: 0.8648 (mp0) cc_final: 0.8158 (mp0) REVERT: D 53 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8007 (ttmm) REVERT: D 382 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8626 (mp0) outliers start: 25 outliers final: 8 residues processed: 123 average time/residue: 2.6107 time to fit residues: 339.1991 Evaluate side-chains 112 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 312 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 89 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3289 r_free = 0.3289 target = 0.089443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.073709 restraints weight = 44832.655| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.84 r_work: 0.2914 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7820 Z= 0.137 Angle : 0.489 5.407 10667 Z= 0.263 Chirality : 0.040 0.141 1246 Planarity : 0.004 0.071 1357 Dihedral : 4.417 32.708 1122 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.98 % Allowed : 24.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.27), residues: 1009 helix: 2.46 (0.27), residues: 391 sheet: 0.45 (0.35), residues: 216 loop : -0.55 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 234 HIS 0.002 0.000 HIS A 230 PHE 0.011 0.001 PHE E 108 TYR 0.009 0.001 TYR D 329 ARG 0.009 0.000 ARG D 270 Details of bonding type rmsd hydrogen bonds : bond 0.03829 ( 398) hydrogen bonds : angle 4.36812 ( 1128) SS BOND : bond 0.00660 ( 6) SS BOND : angle 1.59279 ( 12) covalent geometry : bond 0.00311 ( 7814) covalent geometry : angle 0.48641 (10655) *********************** 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 : 1.216 Fit side-chains revert: symmetry clash REVERT: A 107 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.7821 (tmt-80) REVERT: A 234 SER cc_start: 0.9482 (t) cc_final: 0.9250 (p) REVERT: A 237 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8697 (mt) REVERT: B 87 THR cc_start: 0.8770 (m) cc_final: 0.8565 (p) REVERT: D 16 GLU cc_start: 0.8613 (mp0) cc_final: 0.8134 (mp0) REVERT: D 53 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8126 (ttmm) REVERT: D 382 GLU cc_start: 0.8994 (tp30) cc_final: 0.8607 (mp0) outliers start: 15 outliers final: 6 residues processed: 116 average time/residue: 2.6066 time to fit residues: 319.5045 Evaluate side-chains 108 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain E residue 49 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 61 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3250 r_free = 0.3250 target = 0.087506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.071031 restraints weight = 45586.626| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.89 r_work: 0.2877 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7820 Z= 0.214 Angle : 0.518 6.757 10667 Z= 0.281 Chirality : 0.041 0.143 1246 Planarity : 0.004 0.079 1357 Dihedral : 4.575 34.172 1122 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.78 % Allowed : 24.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.27), residues: 1009 helix: 2.36 (0.27), residues: 385 sheet: 0.36 (0.34), residues: 217 loop : -0.64 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 234 HIS 0.002 0.001 HIS A 230 PHE 0.017 0.001 PHE E 108 TYR 0.011 0.001 TYR D 329 ARG 0.008 0.000 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.04176 ( 398) hydrogen bonds : angle 4.48973 ( 1128) SS BOND : bond 0.00946 ( 6) SS BOND : angle 1.92930 ( 12) covalent geometry : bond 0.00484 ( 7814) covalent geometry : angle 0.51443 (10655) *********************** 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 121 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7815 (tmt-80) REVERT: A 234 SER cc_start: 0.9471 (t) cc_final: 0.9204 (p) REVERT: B 87 THR cc_start: 0.8789 (m) cc_final: 0.8587 (p) REVERT: B 259 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8288 (mt0) REVERT: D 382 GLU cc_start: 0.8964 (tp30) cc_final: 0.8504 (mp0) outliers start: 21 outliers final: 12 residues processed: 117 average time/residue: 2.5064 time to fit residues: 310.0023 Evaluate side-chains 111 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 107 ARG Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 150 ARG 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 B residue 312 ASP Chi-restraints excluded: chain D residue 53 LYS 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 82 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3296 r_free = 0.3296 target = 0.089780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.074022 restraints weight = 45259.736| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.87 r_work: 0.2913 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7820 Z= 0.110 Angle : 0.477 5.205 10667 Z= 0.255 Chirality : 0.040 0.140 1246 Planarity : 0.004 0.078 1357 Dihedral : 4.269 30.310 1122 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.12 % Allowed : 24.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.27), residues: 1009 helix: 2.62 (0.27), residues: 385 sheet: 0.52 (0.34), residues: 213 loop : -0.53 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 234 HIS 0.002 0.000 HIS A 230 PHE 0.014 0.001 PHE D 222 TYR 0.008 0.001 TYR D 329 ARG 0.008 0.000 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.03537 ( 398) hydrogen bonds : angle 4.24013 ( 1128) SS BOND : bond 0.00657 ( 6) SS BOND : angle 1.38884 ( 12) covalent geometry : bond 0.00248 ( 7814) covalent geometry : angle 0.47548 (10655) *********************** 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 125 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 107 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.7794 (tmt-80) REVERT: A 143 TRP cc_start: 0.8248 (t60) cc_final: 0.7472 (t60) REVERT: A 234 SER cc_start: 0.9458 (t) cc_final: 0.9194 (p) REVERT: B 259 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8199 (mt0) REVERT: D 16 GLU cc_start: 0.8598 (mp0) cc_final: 0.8103 (mp0) REVERT: D 382 GLU cc_start: 0.8928 (tp30) cc_final: 0.8522 (mp0) outliers start: 16 outliers final: 7 residues processed: 121 average time/residue: 2.5600 time to fit residues: 327.1569 Evaluate side-chains 105 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 107 ARG 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 259 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3307 r_free = 0.3307 target = 0.090463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.074537 restraints weight = 45257.862| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.87 r_work: 0.2926 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7820 Z= 0.122 Angle : 0.484 5.140 10667 Z= 0.257 Chirality : 0.040 0.135 1246 Planarity : 0.004 0.047 1357 Dihedral : 4.257 32.598 1122 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.51 % Allowed : 24.60 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.27), residues: 1009 helix: 2.68 (0.27), residues: 385 sheet: 0.44 (0.34), residues: 215 loop : -0.53 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 234 HIS 0.001 0.000 HIS A 230 PHE 0.012 0.001 PHE D 222 TYR 0.009 0.001 TYR D 329 ARG 0.004 0.000 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.03457 ( 398) hydrogen bonds : angle 4.20156 ( 1128) SS BOND : bond 0.00606 ( 6) SS BOND : angle 1.44324 ( 12) covalent geometry : bond 0.00278 ( 7814) covalent geometry : angle 0.48152 (10655) *********************** 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 120 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 1.315 Fit side-chains revert: symmetry clash REVERT: A 107 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.7776 (tmt-80) REVERT: A 143 TRP cc_start: 0.8330 (t60) cc_final: 0.7672 (t60) REVERT: A 234 SER cc_start: 0.9449 (t) cc_final: 0.9176 (p) REVERT: A 302 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8390 (mm) REVERT: B 172 GLU cc_start: 0.9169 (tp30) cc_final: 0.8962 (tp30) REVERT: B 259 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8211 (mt0) REVERT: D 16 GLU cc_start: 0.8577 (mp0) cc_final: 0.8123 (mp0) REVERT: D 382 GLU cc_start: 0.8906 (tp30) cc_final: 0.8535 (mp0) outliers start: 19 outliers final: 9 residues processed: 116 average time/residue: 2.5282 time to fit residues: 310.9715 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 : 1.186 ------------------------------------------------------------------------------- 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 107 ARG 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 122 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain E residue 49 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 42 optimal weight: 2.9990 chunk 71 optimal weight: 0.1980 chunk 44 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 181 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 = 0.3306 r_free = 0.3306 target = 0.090417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.074567 restraints weight = 45387.088| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.86 r_work: 0.2927 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7820 Z= 0.126 Angle : 0.483 5.240 10667 Z= 0.257 Chirality : 0.040 0.136 1246 Planarity : 0.004 0.081 1357 Dihedral : 4.220 31.701 1122 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.72 % Allowed : 25.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.27), residues: 1009 helix: 2.71 (0.27), residues: 385 sheet: 0.56 (0.34), residues: 213 loop : -0.50 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 234 HIS 0.001 0.000 HIS A 230 PHE 0.012 0.001 PHE D 222 TYR 0.016 0.001 TYR A 9 ARG 0.009 0.000 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 398) hydrogen bonds : angle 4.18312 ( 1128) SS BOND : bond 0.00615 ( 6) SS BOND : angle 1.46642 ( 12) covalent geometry : bond 0.00287 ( 7814) covalent geometry : angle 0.48095 (10655) *********************** 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 116 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 1.287 Fit side-chains revert: symmetry clash REVERT: A 107 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7769 (tmt-80) REVERT: A 143 TRP cc_start: 0.8295 (t60) cc_final: 0.7635 (t60) REVERT: A 234 SER cc_start: 0.9446 (t) cc_final: 0.9176 (p) REVERT: B 172 GLU cc_start: 0.9170 (tp30) cc_final: 0.8947 (tp30) REVERT: B 259 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8206 (mt0) REVERT: D 16 GLU cc_start: 0.8582 (mp0) cc_final: 0.8121 (mp0) REVERT: D 382 GLU cc_start: 0.8903 (tp30) cc_final: 0.8537 (mp0) outliers start: 13 outliers final: 10 residues processed: 114 average time/residue: 2.3929 time to fit residues: 289.8325 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 : 1.101 ------------------------------------------------------------------------------- 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 107 ARG 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 122 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN 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 0 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 76 optimal weight: 0.0870 chunk 83 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN C 18 GLN E 77 ASN E 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.090480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.074799 restraints weight = 44950.801| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.83 r_work: 0.2929 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7820 Z= 0.129 Angle : 0.490 5.248 10667 Z= 0.260 Chirality : 0.040 0.135 1246 Planarity : 0.004 0.047 1357 Dihedral : 4.201 31.700 1122 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.12 % Allowed : 25.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.27), residues: 1009 helix: 2.73 (0.27), residues: 385 sheet: 0.57 (0.34), residues: 213 loop : -0.50 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 234 HIS 0.002 0.000 HIS A 230 PHE 0.013 0.001 PHE D 222 TYR 0.017 0.001 TYR A 9 ARG 0.004 0.000 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 398) hydrogen bonds : angle 4.17442 ( 1128) SS BOND : bond 0.00614 ( 6) SS BOND : angle 1.45768 ( 12) covalent geometry : bond 0.00294 ( 7814) covalent geometry : angle 0.48750 (10655) *********************** 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 116 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 1.128 Fit side-chains revert: symmetry clash REVERT: A 107 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7755 (tmt-80) REVERT: A 143 TRP cc_start: 0.8355 (t60) cc_final: 0.7903 (t60) REVERT: A 234 SER cc_start: 0.9441 (t) cc_final: 0.9168 (p) REVERT: B 259 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.8235 (mt0) REVERT: D 16 GLU cc_start: 0.8577 (mp0) cc_final: 0.8095 (mp0) REVERT: D 382 GLU cc_start: 0.8900 (tp30) cc_final: 0.8532 (mp0) outliers start: 16 outliers final: 11 residues processed: 114 average time/residue: 2.4981 time to fit residues: 301.0912 Evaluate side-chains 110 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 107 ARG 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 122 SER 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 E residue 49 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 73 optimal weight: 0.0470 chunk 78 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN C 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.090369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.074766 restraints weight = 45440.449| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.86 r_work: 0.2931 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7820 Z= 0.129 Angle : 0.491 5.119 10667 Z= 0.261 Chirality : 0.040 0.134 1246 Planarity : 0.004 0.088 1357 Dihedral : 4.212 32.000 1122 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.72 % Allowed : 26.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.27), residues: 1009 helix: 2.75 (0.27), residues: 385 sheet: 0.55 (0.34), residues: 213 loop : -0.48 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 234 HIS 0.002 0.000 HIS A 230 PHE 0.012 0.001 PHE D 222 TYR 0.021 0.001 TYR A 9 ARG 0.010 0.000 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.03403 ( 398) hydrogen bonds : angle 4.15699 ( 1128) SS BOND : bond 0.00520 ( 6) SS BOND : angle 1.80152 ( 12) covalent geometry : bond 0.00295 ( 7814) covalent geometry : angle 0.48764 (10655) ********************** 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 112 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 1.182 Fit side-chains revert: symmetry clash REVERT: A 107 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7754 (tmt-80) REVERT: A 143 TRP cc_start: 0.8325 (t60) cc_final: 0.7852 (t60) REVERT: A 234 SER cc_start: 0.9436 (t) cc_final: 0.9164 (p) REVERT: B 259 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8246 (mt0) REVERT: D 16 GLU cc_start: 0.8566 (mp0) cc_final: 0.8093 (mp0) REVERT: D 382 GLU cc_start: 0.8901 (tp30) cc_final: 0.8535 (mp0) outliers start: 13 outliers final: 9 residues processed: 110 average time/residue: 2.4385 time to fit residues: 284.6205 Evaluate side-chains 107 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 107 ARG 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 E residue 49 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 61 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 284 ASN C 18 GLN E 77 ASN E 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.088962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.073465 restraints weight = 45594.679| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.84 r_work: 0.2902 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7820 Z= 0.174 Angle : 0.512 6.389 10667 Z= 0.274 Chirality : 0.040 0.137 1246 Planarity : 0.004 0.079 1357 Dihedral : 4.345 33.585 1122 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.98 % Allowed : 25.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.27), residues: 1009 helix: 2.65 (0.27), residues: 385 sheet: 0.45 (0.34), residues: 215 loop : -0.52 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 234 HIS 0.002 0.000 HIS A 230 PHE 0.015 0.001 PHE E 108 TYR 0.023 0.001 TYR A 9 ARG 0.008 0.000 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 398) hydrogen bonds : angle 4.26816 ( 1128) SS BOND : bond 0.00779 ( 6) SS BOND : angle 2.13604 ( 12) covalent geometry : bond 0.00396 ( 7814) covalent geometry : angle 0.50681 (10655) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11204.23 seconds wall clock time: 191 minutes 59.38 seconds (11519.38 seconds total)