Starting phenix.real_space_refine on Fri Jun 13 05:16:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ee8_47951/06_2025/9ee8_47951.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ee8_47951/06_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_47951/06_2025/9ee8_47951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ee8_47951/06_2025/9ee8_47951.map" model { file = "/net/cci-nas-00/data/ceres_data/9ee8_47951/06_2025/9ee8_47951.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ee8_47951/06_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-5710/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: 8.05, 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: 3.68 Conformation dependent library (CDL) restraints added in 1.2 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: 1.29 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: 5.40 Time building geometry restraints manager: 4.50 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: 26676 2.19 - 4.37: 167 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: 865 0.035 - 0.070: 254 0.070 - 0.104: 78 0.104 - 0.139: 45 0.139 - 0.174: 4 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: 2.310 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: 0.280 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 34.700 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:13.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.730 ------------------------------------------------------------------------------- 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= 0.296 Angle : 0.610 9.945 10667 Z= 0.370 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 0.00458 ( 7814) covalent geometry : angle 0.60758 (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 : 1.232 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: 2.5573 time to fit residues: 394.6092 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 : 1.130 ------------------------------------------------------------------------------- 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 = 0.3320 r_free = 0.3320 target = 0.091525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.075555 restraints weight = 44428.024| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.83 r_work: 0.2927 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1399 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= 0.173 Angle : 0.522 6.121 10667 Z= 0.282 Chirality : 0.041 0.146 1246 Planarity : 0.004 0.048 1357 Dihedral : 4.776 39.962 1122 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.38 % Allowed : 24.87 % 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: 1.35 (0.28), residues: 1009 helix: 2.53 (0.27), residues: 392 sheet: 0.56 (0.36), residues: 210 loop : -0.55 (0.31), residues: 407 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 0.009 0.001 TYR D 329 ARG 0.007 0.001 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.04366 ( 398) hydrogen bonds : angle 4.63368 ( 1128) SS BOND : bond 0.00730 ( 6) SS BOND : angle 1.50247 ( 12) covalent geometry : bond 0.00384 ( 7814) covalent geometry : angle 0.51956 (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: 18 poor density : 118 time to evaluate : 1.293 Fit side-chains revert: symmetry clash REVERT: A 107 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.7861 (tmt-80) REVERT: A 211 MET cc_start: 0.7376 (mtp) cc_final: 0.7103 (mtp) REVERT: A 234 SER cc_start: 0.9503 (t) cc_final: 0.9266 (p) REVERT: B 234 PHE cc_start: 0.9244 (OUTLIER) cc_final: 0.8463 (t80) REVERT: C 36 ASP cc_start: 0.8968 (m-30) cc_final: 0.8737 (m-30) REVERT: D 16 GLU cc_start: 0.8648 (mp0) cc_final: 0.8252 (mp0) REVERT: D 27 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8440 (mm-30) REVERT: D 208 PHE cc_start: 0.8110 (m-80) cc_final: 0.7638 (m-80) REVERT: D 382 GLU cc_start: 0.8998 (tp30) cc_final: 0.8575 (mp0) outliers start: 18 outliers final: 7 residues processed: 130 average time/residue: 2.6980 time to fit residues: 373.3680 Evaluate side-chains 115 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 D residue 239 ASN Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 11 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3291 r_free = 0.3291 target = 0.089567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.073792 restraints weight = 44970.769| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.83 r_work: 0.2920 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7820 Z= 0.180 Angle : 0.506 6.138 10667 Z= 0.274 Chirality : 0.041 0.140 1246 Planarity : 0.004 0.051 1357 Dihedral : 4.532 35.232 1122 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.51 % Allowed : 24.07 % 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: 1.24 (0.27), residues: 1009 helix: 2.45 (0.27), residues: 391 sheet: 0.38 (0.35), residues: 218 loop : -0.56 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 234 HIS 0.002 0.001 HIS A 230 PHE 0.014 0.001 PHE E 108 TYR 0.010 0.001 TYR D 329 ARG 0.004 0.000 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.04128 ( 398) hydrogen bonds : angle 4.48399 ( 1128) SS BOND : bond 0.00804 ( 6) SS BOND : angle 1.79675 ( 12) covalent geometry : bond 0.00406 ( 7814) covalent geometry : angle 0.50264 (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 127 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 1.235 Fit side-chains revert: symmetry clash REVERT: A 107 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.7833 (tmt-80) REVERT: A 211 MET cc_start: 0.7400 (mtp) cc_final: 0.7193 (mtp) REVERT: A 234 SER cc_start: 0.9496 (t) cc_final: 0.9282 (p) REVERT: A 237 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8688 (mt) REVERT: B 87 THR cc_start: 0.8783 (m) cc_final: 0.8579 (p) REVERT: D 16 GLU cc_start: 0.8624 (mp0) cc_final: 0.8163 (mp0) REVERT: D 27 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8426 (mt-10) REVERT: D 53 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8034 (ttmm) REVERT: D 208 PHE cc_start: 0.8120 (m-80) cc_final: 0.7909 (m-80) REVERT: D 382 GLU cc_start: 0.9018 (tp30) cc_final: 0.8634 (mp0) outliers start: 19 outliers final: 9 residues processed: 120 average time/residue: 2.9060 time to fit residues: 370.1497 Evaluate side-chains 114 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 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 279 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 49 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 89 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.090802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.075067 restraints weight = 44654.920| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.83 r_work: 0.2932 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7820 Z= 0.104 Angle : 0.466 4.748 10667 Z= 0.250 Chirality : 0.039 0.141 1246 Planarity : 0.004 0.071 1357 Dihedral : 4.195 30.866 1122 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.12 % Allowed : 24.60 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.43 (0.28), residues: 1009 helix: 2.65 (0.27), residues: 391 sheet: 0.48 (0.35), residues: 215 loop : -0.49 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 234 HIS 0.002 0.000 HIS D 220 PHE 0.009 0.001 PHE A 182 TYR 0.008 0.001 TYR D 329 ARG 0.011 0.000 ARG D 270 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 398) hydrogen bonds : angle 4.23185 ( 1128) SS BOND : bond 0.00383 ( 6) SS BOND : angle 1.33552 ( 12) covalent geometry : bond 0.00232 ( 7814) covalent geometry : angle 0.46399 (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 123 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 1.284 Fit side-chains REVERT: A 107 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.7797 (tmt-80) REVERT: A 211 MET cc_start: 0.7323 (mtp) cc_final: 0.7074 (mtp) REVERT: A 234 SER cc_start: 0.9493 (t) cc_final: 0.9275 (p) REVERT: A 237 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8701 (mt) REVERT: B 234 PHE cc_start: 0.9265 (OUTLIER) cc_final: 0.8524 (t80) REVERT: D 16 GLU cc_start: 0.8631 (mp0) cc_final: 0.8200 (mp0) REVERT: D 27 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8420 (mt-10) REVERT: D 53 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7979 (ttmm) REVERT: D 382 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8605 (mp0) outliers start: 16 outliers final: 6 residues processed: 116 average time/residue: 2.4801 time to fit residues: 305.0399 Evaluate side-chains 114 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 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 279 SER Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain E residue 3 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 61 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 82 optimal weight: 0.1980 chunk 2 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 = 0.089538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.073564 restraints weight = 45274.605| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.83 r_work: 0.2915 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7820 Z= 0.171 Angle : 0.494 6.170 10667 Z= 0.266 Chirality : 0.040 0.136 1246 Planarity : 0.004 0.076 1357 Dihedral : 4.359 34.065 1122 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.91 % Allowed : 24.07 % 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: 1.32 (0.27), residues: 1009 helix: 2.54 (0.27), residues: 391 sheet: 0.45 (0.34), residues: 216 loop : -0.55 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 234 HIS 0.002 0.001 HIS A 230 PHE 0.015 0.001 PHE A 182 TYR 0.010 0.001 TYR D 329 ARG 0.008 0.000 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 398) hydrogen bonds : angle 4.33240 ( 1128) SS BOND : bond 0.00830 ( 6) SS BOND : angle 1.73975 ( 12) covalent geometry : bond 0.00388 ( 7814) covalent geometry : angle 0.49046 (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 125 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 1.184 Fit side-chains revert: symmetry clash REVERT: A 107 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7787 (tmt-80) REVERT: A 234 SER cc_start: 0.9481 (t) cc_final: 0.9211 (p) REVERT: B 87 THR cc_start: 0.8759 (m) cc_final: 0.8553 (p) REVERT: B 259 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8275 (mt0) REVERT: D 16 GLU cc_start: 0.8607 (mp0) cc_final: 0.8119 (mp0) REVERT: D 27 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8424 (mt-10) REVERT: D 53 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8080 (ttmm) REVERT: D 382 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8603 (mp0) outliers start: 22 outliers final: 9 residues processed: 118 average time/residue: 2.4434 time to fit residues: 305.9498 Evaluate side-chains 111 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 279 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 82 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 1 optimal weight: 0.1980 chunk 37 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3323 r_free = 0.3323 target = 0.091409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.075680 restraints weight = 44983.030| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.87 r_work: 0.2935 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7820 Z= 0.097 Angle : 0.463 4.212 10667 Z= 0.247 Chirality : 0.039 0.139 1246 Planarity : 0.004 0.078 1357 Dihedral : 4.111 30.526 1122 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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: 1.53 (0.28), residues: 1009 helix: 2.76 (0.27), residues: 391 sheet: 0.49 (0.35), residues: 215 loop : -0.45 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 234 HIS 0.001 0.000 HIS D 220 PHE 0.013 0.001 PHE A 182 TYR 0.008 0.001 TYR D 329 ARG 0.008 0.000 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.03273 ( 398) hydrogen bonds : angle 4.11485 ( 1128) SS BOND : bond 0.00451 ( 6) SS BOND : angle 1.23981 ( 12) covalent geometry : bond 0.00217 ( 7814) covalent geometry : angle 0.46095 (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 128 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 1.299 Fit side-chains revert: symmetry clash REVERT: A 107 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.7759 (tmt-80) REVERT: A 234 SER cc_start: 0.9459 (t) cc_final: 0.9189 (p) REVERT: B 87 THR cc_start: 0.8746 (m) cc_final: 0.8542 (p) REVERT: B 259 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8189 (mt0) REVERT: D 16 GLU cc_start: 0.8616 (mp0) cc_final: 0.8202 (mp0) REVERT: D 27 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8363 (mm-30) REVERT: D 53 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8132 (ttmm) REVERT: D 382 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8574 (mp0) outliers start: 21 outliers final: 11 residues processed: 122 average time/residue: 2.3133 time to fit residues: 300.4261 Evaluate side-chains 119 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 B residue 279 SER Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 49 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.3286 r_free = 0.3286 target = 0.089167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.073517 restraints weight = 45506.721| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.84 r_work: 0.2914 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7820 Z= 0.182 Angle : 0.502 6.108 10667 Z= 0.268 Chirality : 0.040 0.138 1246 Planarity : 0.004 0.084 1357 Dihedral : 4.307 33.187 1122 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.38 % Allowed : 24.74 % 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: 1.36 (0.27), residues: 1009 helix: 2.66 (0.27), residues: 385 sheet: 0.44 (0.34), residues: 217 loop : -0.55 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 234 HIS 0.002 0.001 HIS A 230 PHE 0.016 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 0.03750 ( 398) hydrogen bonds : angle 4.28209 ( 1128) SS BOND : bond 0.00815 ( 6) SS BOND : angle 1.68808 ( 12) covalent geometry : bond 0.00409 ( 7814) covalent geometry : angle 0.49873 (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 116 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.7806 (tmt-80) REVERT: A 234 SER cc_start: 0.9465 (t) cc_final: 0.9194 (p) REVERT: B 172 GLU cc_start: 0.9172 (tp30) cc_final: 0.8939 (tp30) REVERT: B 259 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8282 (mt0) REVERT: D 16 GLU cc_start: 0.8601 (mp0) cc_final: 0.8145 (mp0) REVERT: D 27 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8440 (mt-10) REVERT: D 382 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8575 (mp0) outliers start: 18 outliers final: 12 residues processed: 112 average time/residue: 2.6768 time to fit residues: 318.5486 Evaluate side-chains 110 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 1.247 ------------------------------------------------------------------------------- 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 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=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: 0.8980 chunk 5 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3310 r_free = 0.3310 target = 0.090749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.075034 restraints weight = 45159.778| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.87 r_work: 0.2939 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7820 Z= 0.099 Angle : 0.466 4.277 10667 Z= 0.248 Chirality : 0.039 0.137 1246 Planarity : 0.004 0.075 1357 Dihedral : 4.090 30.882 1122 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.98 % Allowed : 24.74 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.53 (0.28), residues: 1009 helix: 2.84 (0.27), residues: 385 sheet: 0.50 (0.34), residues: 215 loop : -0.48 (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 0.017 0.001 PHE A 182 TYR 0.008 0.001 TYR D 329 ARG 0.008 0.000 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.03232 ( 398) hydrogen bonds : angle 4.07614 ( 1128) SS BOND : bond 0.00480 ( 6) SS BOND : angle 1.24443 ( 12) covalent geometry : bond 0.00220 ( 7814) covalent geometry : angle 0.46430 (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 124 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 1.289 Fit side-chains revert: symmetry clash REVERT: A 234 SER cc_start: 0.9447 (t) cc_final: 0.9182 (p) REVERT: A 302 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8397 (mm) REVERT: B 259 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8224 (mt0) REVERT: D 16 GLU cc_start: 0.8614 (mp0) cc_final: 0.8187 (mp0) REVERT: D 382 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8562 (mp0) outliers start: 15 outliers final: 9 residues processed: 120 average time/residue: 2.5108 time to fit residues: 321.4575 Evaluate side-chains 111 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain D residue 382 GLU 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: 2.9990 chunk 76 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 80 optimal weight: 0.2980 chunk 58 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 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 = 0.3300 r_free = 0.3300 target = 0.090262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.074383 restraints weight = 44915.983| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.84 r_work: 0.2929 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2532 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= 0.140 Angle : 0.490 5.134 10667 Z= 0.260 Chirality : 0.040 0.132 1246 Planarity : 0.004 0.089 1357 Dihedral : 4.134 31.335 1122 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.38 % Allowed : 24.87 % 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: 1.51 (0.27), residues: 1009 helix: 2.77 (0.27), residues: 385 sheet: 0.59 (0.34), residues: 213 loop : -0.51 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 234 HIS 0.002 0.000 HIS A 230 PHE 0.021 0.001 PHE A 182 TYR 0.009 0.001 TYR D 329 ARG 0.011 0.000 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.03422 ( 398) hydrogen bonds : angle 4.15569 ( 1128) SS BOND : bond 0.00689 ( 6) SS BOND : angle 1.45337 ( 12) covalent geometry : bond 0.00318 ( 7814) covalent geometry : angle 0.48809 (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 117 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 1.338 Fit side-chains revert: symmetry clash REVERT: A 107 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.7781 (tmt-80) REVERT: A 234 SER cc_start: 0.9455 (t) cc_final: 0.9189 (p) REVERT: A 302 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8388 (mm) REVERT: B 259 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8204 (mt0) REVERT: D 16 GLU cc_start: 0.8575 (mp0) cc_final: 0.8122 (mp0) REVERT: D 382 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8552 (mp0) outliers start: 18 outliers final: 10 residues processed: 113 average time/residue: 2.5873 time to fit residues: 310.1947 Evaluate side-chains 110 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 1.276 ------------------------------------------------------------------------------- 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 A residue 302 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain D residue 382 GLU 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: 0.9980 chunk 25 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 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 = 0.3289 r_free = 0.3289 target = 0.089421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.073729 restraints weight = 45553.173| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.87 r_work: 0.2908 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7820 Z= 0.159 Angle : 0.500 5.570 10667 Z= 0.268 Chirality : 0.040 0.136 1246 Planarity : 0.004 0.087 1357 Dihedral : 4.264 32.894 1122 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.25 % Allowed : 25.13 % Favored : 72.62 % 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: 1.47 (0.27), residues: 1009 helix: 2.70 (0.27), residues: 385 sheet: 0.58 (0.34), residues: 214 loop : -0.49 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 234 HIS 0.002 0.000 HIS A 230 PHE 0.024 0.001 PHE A 182 TYR 0.023 0.001 TYR A 9 ARG 0.010 0.000 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 398) hydrogen bonds : angle 4.22136 ( 1128) SS BOND : bond 0.00741 ( 6) SS BOND : angle 1.58398 ( 12) covalent geometry : bond 0.00361 ( 7814) covalent geometry : angle 0.49776 (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 114 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 1.451 Fit side-chains revert: symmetry clash REVERT: A 107 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.7771 (tmt-80) REVERT: A 234 SER cc_start: 0.9454 (t) cc_final: 0.9192 (p) REVERT: B 259 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8255 (mt0) REVERT: D 16 GLU cc_start: 0.8580 (mp0) cc_final: 0.8124 (mp0) REVERT: D 382 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8563 (mp0) outliers start: 17 outliers final: 11 residues processed: 109 average time/residue: 2.7054 time to fit residues: 314.8578 Evaluate side-chains 109 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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 B residue 279 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain D residue 382 GLU 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: 0.9980 chunk 6 optimal weight: 0.0670 chunk 94 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 0.0070 chunk 18 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 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 = 0.3302 r_free = 0.3302 target = 0.090319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.074665 restraints weight = 45123.981| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.86 r_work: 0.2928 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7820 Z= 0.107 Angle : 0.486 4.981 10667 Z= 0.257 Chirality : 0.040 0.141 1246 Planarity : 0.004 0.084 1357 Dihedral : 4.141 31.452 1122 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.72 % Allowed : 25.66 % Favored : 72.62 % 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: 1.58 (0.27), residues: 1009 helix: 2.80 (0.27), residues: 385 sheet: 0.60 (0.34), residues: 213 loop : -0.42 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 234 HIS 0.002 0.000 HIS B 311 PHE 0.018 0.001 PHE A 182 TYR 0.023 0.001 TYR A 9 ARG 0.010 0.000 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.03337 ( 398) hydrogen bonds : angle 4.13317 ( 1128) SS BOND : bond 0.00537 ( 6) SS BOND : angle 1.33194 ( 12) covalent geometry : bond 0.00242 ( 7814) covalent geometry : angle 0.48415 (10655) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13133.35 seconds wall clock time: 229 minutes 8.40 seconds (13748.40 seconds total)