Starting phenix.real_space_refine on Wed Aug 5 09:34:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ygz_72946/08_2026/9ygz_72946.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ygz_72946/08_2026/9ygz_72946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ygz_72946/08_2026/9ygz_72946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ygz_72946/08_2026/9ygz_72946.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ygz_72946/08_2026/9ygz_72946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ygz_72946/08_2026/9ygz_72946.map" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 5773 2.51 5 N 1544 2.21 5 O 1664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9043 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2384 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 18, 'TRANS': 282} Chain: "B" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2558 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "H" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1785 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "A" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1867 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.41, per 1000 atoms: 0.16 Number of scatterers: 9043 At special positions: 0 Unit cell: (118.422, 111.996, 134.946, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1664 8.00 N 1544 7.00 C 5773 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 126 " - pdb=" SG CYS R 203 " distance=2.05 Simple disulfide: pdb=" SG CYS H 39 " - pdb=" SG CYS H 113 " distance=2.04 Simple disulfide: pdb=" SG CYS H 176 " - pdb=" SG CYS H 246 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 250.9 milliseconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2146 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 37.0% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'R' and resid 49 through 81 removed outlier: 4.067A pdb=" N TYR R 53 " --> pdb=" O PRO R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 88 No H-bonds generated for 'chain 'R' and resid 86 through 88' Processing helix chain 'R' and resid 89 through 114 removed outlier: 3.573A pdb=" N VAL R 93 " --> pdb=" O ASN R 89 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE R 109 " --> pdb=" O ILE R 105 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL R 112 " --> pdb=" O THR R 108 " (cutoff:3.500A) Processing helix chain 'R' and resid 122 through 157 removed outlier: 3.573A pdb=" N ALA R 145 " --> pdb=" O LEU R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 184 removed outlier: 3.625A pdb=" N ALA R 169 " --> pdb=" O ASP R 165 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL R 171 " --> pdb=" O LYS R 167 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA R 174 " --> pdb=" O ILE R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 190 Processing helix chain 'R' and resid 215 through 228 removed outlier: 3.515A pdb=" N ILE R 221 " --> pdb=" O GLN R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 251 removed outlier: 3.632A pdb=" N VAL R 249 " --> pdb=" O ALA R 245 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS R 251 " --> pdb=" O ARG R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 256 through 282 removed outlier: 3.554A pdb=" N VAL R 271 " --> pdb=" O THR R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 293 removed outlier: 3.853A pdb=" N PHE R 287 " --> pdb=" O PRO R 283 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 304 No H-bonds generated for 'chain 'R' and resid 302 through 304' Processing helix chain 'R' and resid 305 through 323 removed outlier: 3.643A pdb=" N PHE R 309 " --> pdb=" O ALA R 305 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA R 314 " --> pdb=" O PHE R 310 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N THR R 315 " --> pdb=" O ALA R 311 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ILE R 316 " --> pdb=" O LYS R 312 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR R 317 " --> pdb=" O SER R 313 " (cutoff:3.500A) Proline residue: R 319 - end of helix Processing helix chain 'R' and resid 326 through 334 Processing helix chain 'B' and resid 10 through 25 removed outlier: 3.835A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.558A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.755A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' Processing helix chain 'H' and resid 104 through 108 removed outlier: 3.754A pdb=" N THR H 108 " --> pdb=" O SER H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 241 removed outlier: 4.027A pdb=" N VAL H 241 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.612A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.793A pdb=" N ILE A 49 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.508A pdb=" N GLN A 202 " --> pdb=" O LYS A 199 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN A 205 " --> pdb=" O GLN A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 234 Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.533A pdb=" N LEU A 238 " --> pdb=" O ASN A 235 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG A 239 " --> pdb=" O ARG A 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 235 through 239' Processing helix chain 'A' and resid 249 through 260 removed outlier: 3.512A pdb=" N LEU A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'A' and resid 268 through 274 Processing helix chain 'A' and resid 287 through 307 removed outlier: 3.500A pdb=" N THR A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA A 307 " --> pdb=" O ARG A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 347 removed outlier: 3.762A pdb=" N ARG A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 331 " --> pdb=" O ASN A 327 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 194 through 197 removed outlier: 4.451A pdb=" N SER R 202 " --> pdb=" O HIS R 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.710A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.045A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.018A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.844A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.986A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.958A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.728A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 20 through 24 removed outlier: 3.538A pdb=" N SER H 88 " --> pdb=" O PHE H 97 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 27 through 29 removed outlier: 6.040A pdb=" N GLY H 27 " --> pdb=" O THR H 135 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N MET H 51 " --> pdb=" O TYR H 67 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N TYR H 67 " --> pdb=" O MET H 51 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TRP H 53 " --> pdb=" O VAL H 65 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 157 through 159 Processing sheet with id=AB3, first strand: chain 'H' and resid 163 through 165 removed outlier: 6.793A pdb=" N TRP H 193 " --> pdb=" O LEU H 205 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 163 through 165 removed outlier: 4.111A pdb=" N THR H 255 " --> pdb=" O GLN H 248 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 175 through 180 removed outlier: 6.437A pdb=" N HIS A 34 " --> pdb=" O HIS A 186 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N PHE A 188 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU A 36 " --> pdb=" O PHE A 188 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA A 209 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE A 210 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N PHE A 246 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N PHE A 212 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ASN A 248 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL A 214 " --> pdb=" O ASN A 248 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1149 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1485 1.31 - 1.44: 2664 1.44 - 1.56: 5020 1.56 - 1.69: 0 1.69 - 1.82: 89 Bond restraints: 9258 Sorted by residual: bond pdb=" C ASP A 228 " pdb=" O ASP A 228 " ideal model delta sigma weight residual 1.237 1.185 0.051 1.17e-02 7.31e+03 1.93e+01 bond pdb=" CA PHE R 299 " pdb=" C PHE R 299 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.25e-02 6.40e+03 1.53e+01 bond pdb=" CA SER R 256 " pdb=" C SER R 256 " ideal model delta sigma weight residual 1.523 1.473 0.050 1.30e-02 5.92e+03 1.48e+01 bond pdb=" C LEU R 306 " pdb=" O LEU R 306 " ideal model delta sigma weight residual 1.244 1.208 0.036 9.40e-03 1.13e+04 1.45e+01 bond pdb=" CA VAL R 63 " pdb=" C VAL R 63 " ideal model delta sigma weight residual 1.523 1.478 0.045 1.27e-02 6.20e+03 1.27e+01 ... (remaining 9253 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 11898 1.62 - 3.24: 589 3.24 - 4.86: 60 4.86 - 6.49: 14 6.49 - 8.11: 6 Bond angle restraints: 12567 Sorted by residual: angle pdb=" C TYR R 213 " pdb=" N PRO R 214 " pdb=" CA PRO R 214 " ideal model delta sigma weight residual 119.84 125.95 -6.11 1.25e+00 6.40e-01 2.39e+01 angle pdb=" N VAL R 216 " pdb=" CA VAL R 216 " pdb=" C VAL R 216 " ideal model delta sigma weight residual 110.42 114.97 -4.55 9.60e-01 1.09e+00 2.25e+01 angle pdb=" CA THR R 230 " pdb=" C THR R 230 " pdb=" N PRO R 231 " ideal model delta sigma weight residual 120.52 116.89 3.63 8.30e-01 1.45e+00 1.91e+01 angle pdb=" C TYR R 297 " pdb=" N PRO R 298 " pdb=" CA PRO R 298 " ideal model delta sigma weight residual 119.93 124.56 -4.63 1.07e+00 8.73e-01 1.88e+01 angle pdb=" C GLY R 38 " pdb=" N PRO R 39 " pdb=" CA PRO R 39 " ideal model delta sigma weight residual 119.56 123.94 -4.38 1.02e+00 9.61e-01 1.85e+01 ... (remaining 12562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 5051 17.96 - 35.93: 288 35.93 - 53.89: 94 53.89 - 71.85: 14 71.85 - 89.82: 11 Dihedral angle restraints: 5458 sinusoidal: 2126 harmonic: 3332 Sorted by residual: dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 162.34 17.66 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CG ARG B 214 " pdb=" CD ARG B 214 " pdb=" NE ARG B 214 " pdb=" CZ ARG B 214 " ideal model delta sinusoidal sigma weight residual 90.00 40.73 49.27 2 1.50e+01 4.44e-03 1.22e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 162.91 17.09 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 5455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1135 0.075 - 0.150: 230 0.150 - 0.225: 26 0.225 - 0.299: 3 0.299 - 0.374: 1 Chirality restraints: 1395 Sorted by residual: chirality pdb=" CA LEU R 306 " pdb=" N LEU R 306 " pdb=" C LEU R 306 " pdb=" CB LEU R 306 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CA ARG B 256 " pdb=" N ARG B 256 " pdb=" C ARG B 256 " pdb=" CB ARG B 256 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA TYR R 317 " pdb=" N TYR R 317 " pdb=" C TYR R 317 " pdb=" CB TYR R 317 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1392 not shown) Planarity restraints: 1597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 317 " -0.053 2.00e-02 2.50e+03 2.70e-02 1.45e+01 pdb=" CG TYR R 317 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR R 317 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR R 317 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR R 317 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR R 317 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR R 317 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR R 317 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY R 42 " -0.057 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO R 43 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO R 43 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO R 43 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP R 183 " 0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C TRP R 183 " -0.058 2.00e-02 2.50e+03 pdb=" O TRP R 183 " 0.021 2.00e-02 2.50e+03 pdb=" N THR R 184 " 0.020 2.00e-02 2.50e+03 ... (remaining 1594 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 3671 2.91 - 3.41: 7901 3.41 - 3.90: 13855 3.90 - 4.40: 15847 4.40 - 4.90: 27680 Nonbonded interactions: 68954 Sorted by model distance: nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.409 3.040 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.416 3.040 nonbonded pdb=" OD1 ASP B 228 " pdb=" NH2 ARG A 198 " model vdw 2.418 3.120 nonbonded pdb=" NZ LYS B 57 " pdb=" OD1 ASN A 205 " model vdw 2.432 3.120 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.432 3.040 ... (remaining 68949 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: 1.300 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 6.690 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 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 : 0.011 0.452 9262 Z= 0.764 Angle : 0.799 8.107 12573 Z= 0.532 Chirality : 0.060 0.374 1395 Planarity : 0.006 0.087 1597 Dihedral : 13.598 89.816 3303 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.94 % Favored : 97.89 % Rotamer: Outliers : 1.02 % Allowed : 8.50 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.24), residues: 1136 helix: 1.38 (0.26), residues: 368 sheet: 1.02 (0.31), residues: 280 loop : -0.48 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 214 TYR 0.053 0.003 TYR R 317 PHE 0.025 0.002 PHE R 119 TRP 0.022 0.003 TRP R 195 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00941 / 0.60 ( 9258) covalent geometry : angle 0.79636 / 0.53 (12567) SS BOND : bond 0.00977 / 0.48 ( 3) SS BOND : angle 2.88732 / 1.36 ( 6) hydrogen bonds : bond 0.19575 / 12.72 ( 413) hydrogen bonds : angle 6.02972 / 4.51 ( 1149) Misc. bond : bond 0.45224 / 23.80 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 164 time to evaluate : 0.340 Fit side-chains REVERT: R 255 GLU cc_start: 0.6843 (mp0) cc_final: 0.6576 (mm-30) REVERT: B 96 ARG cc_start: 0.7755 (mtp180) cc_final: 0.7430 (mtt90) REVERT: B 184 THR cc_start: 0.8976 (m) cc_final: 0.8764 (m) REVERT: B 197 ARG cc_start: 0.7961 (mtt180) cc_final: 0.7423 (mtp-110) REVERT: B 234 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8420 (m-80) REVERT: B 325 MET cc_start: 0.8783 (tpp) cc_final: 0.8077 (mmt) REVERT: A 28 GLN cc_start: 0.8581 (mt0) cc_final: 0.8335 (mt0) REVERT: A 175 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7632 (tm-30) REVERT: A 334 ASP cc_start: 0.8370 (m-30) cc_final: 0.7941 (m-30) outliers start: 10 outliers final: 5 residues processed: 171 average time/residue: 0.0761 time to fit residues: 18.1705 Evaluate side-chains 129 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 123 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain A residue 308 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.0980 chunk 106 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 114 GLN B 62 HIS B 295 ASN A 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.165061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.126096 restraints weight = 10296.713| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.02 r_work: 0.3240 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9262 Z= 0.174 Angle : 0.619 7.036 12573 Z= 0.331 Chirality : 0.045 0.172 1395 Planarity : 0.005 0.054 1597 Dihedral : 5.484 76.079 1268 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.77 % Allowed : 8.09 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.24), residues: 1136 helix: 2.05 (0.26), residues: 372 sheet: 1.06 (0.31), residues: 272 loop : -0.48 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 150 TYR 0.033 0.002 TYR H 207 PHE 0.018 0.002 PHE A 296 TRP 0.014 0.002 TRP B 82 HIS 0.007 0.002 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 9258) covalent geometry : angle 0.61797 / 0.33 (12567) SS BOND : bond 0.00828 / 0.36 ( 3) SS BOND : angle 1.84142 / 1.02 ( 6) hydrogen bonds : bond 0.06880 / 4.40 ( 413) hydrogen bonds : angle 4.54816 / 3.42 ( 1149) Misc. bond : bond 0.00111 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.231 Fit side-chains REVERT: R 255 GLU cc_start: 0.7195 (mp0) cc_final: 0.6817 (mm-30) REVERT: R 303 MET cc_start: 0.6247 (tpp) cc_final: 0.5853 (ttp) REVERT: B 96 ARG cc_start: 0.8219 (mtp180) cc_final: 0.7672 (mtt180) REVERT: B 197 ARG cc_start: 0.8394 (mtt180) cc_final: 0.7876 (mtp-110) REVERT: B 234 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8630 (m-80) REVERT: B 325 MET cc_start: 0.8952 (tpp) cc_final: 0.8210 (mmt) REVERT: G 20 LYS cc_start: 0.7170 (mttt) cc_final: 0.6687 (mtmt) REVERT: G 21 MET cc_start: 0.4942 (mmt) cc_final: 0.4677 (mmt) REVERT: H 68 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8429 (tp) REVERT: A 175 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7558 (tm-30) REVERT: A 300 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7936 (mm-30) REVERT: A 334 ASP cc_start: 0.8490 (m-30) cc_final: 0.8149 (m-30) outliers start: 27 outliers final: 16 residues processed: 138 average time/residue: 0.0849 time to fit residues: 16.1525 Evaluate side-chains 127 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain R residue 203 CYS Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 179 GLN Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 342 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 52 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 61 optimal weight: 0.4980 chunk 50 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.165247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.125579 restraints weight = 10251.276| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.03 r_work: 0.3243 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9262 Z= 0.146 Angle : 0.563 7.295 12573 Z= 0.303 Chirality : 0.043 0.162 1395 Planarity : 0.005 0.046 1597 Dihedral : 5.229 66.078 1262 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.56 % Allowed : 10.35 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.24), residues: 1136 helix: 2.23 (0.26), residues: 370 sheet: 1.06 (0.31), residues: 275 loop : -0.42 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.025 0.002 TYR H 207 PHE 0.016 0.001 PHE R 290 TRP 0.015 0.001 TRP H 64 HIS 0.005 0.001 HIS H 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 9258) covalent geometry : angle 0.56207 / 0.30 (12567) SS BOND : bond 0.00837 / 0.37 ( 3) SS BOND : angle 1.22896 / 0.66 ( 6) hydrogen bonds : bond 0.06304 / 4.06 ( 413) hydrogen bonds : angle 4.35672 / 3.29 ( 1149) Misc. bond : bond 0.00002 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.264 Fit side-chains REVERT: R 255 GLU cc_start: 0.7320 (mp0) cc_final: 0.6886 (mm-30) REVERT: B 59 TYR cc_start: 0.8933 (OUTLIER) cc_final: 0.8401 (m-80) REVERT: B 96 ARG cc_start: 0.8293 (mtp180) cc_final: 0.7678 (mtt180) REVERT: B 197 ARG cc_start: 0.8401 (mtt180) cc_final: 0.7845 (mtp-110) REVERT: B 234 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.8618 (m-80) REVERT: B 308 LEU cc_start: 0.8187 (mt) cc_final: 0.7986 (mp) REVERT: G 20 LYS cc_start: 0.7383 (mttt) cc_final: 0.7004 (mtmt) REVERT: H 51 MET cc_start: 0.9052 (mmm) cc_final: 0.8802 (mmt) REVERT: H 68 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8312 (tp) REVERT: A 175 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7604 (tm-30) REVERT: A 220 ASN cc_start: 0.8539 (m-40) cc_final: 0.8192 (m-40) REVERT: A 334 ASP cc_start: 0.8469 (m-30) cc_final: 0.8108 (m-30) outliers start: 25 outliers final: 19 residues processed: 129 average time/residue: 0.0894 time to fit residues: 15.7207 Evaluate side-chains 130 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain R residue 203 CYS Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 179 GLN Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 342 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 41 optimal weight: 0.9980 chunk 104 optimal weight: 0.2980 chunk 29 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.167407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.127997 restraints weight = 10422.192| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.05 r_work: 0.3253 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9262 Z= 0.126 Angle : 0.523 7.884 12573 Z= 0.282 Chirality : 0.042 0.159 1395 Planarity : 0.004 0.046 1597 Dihedral : 5.255 84.999 1262 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.46 % Allowed : 10.66 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.24), residues: 1136 helix: 2.40 (0.27), residues: 369 sheet: 1.00 (0.31), residues: 273 loop : -0.35 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 150 TYR 0.024 0.001 TYR H 207 PHE 0.011 0.001 PHE B 199 TRP 0.014 0.001 TRP H 64 HIS 0.004 0.001 HIS A 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 9258) covalent geometry : angle 0.52278 / 0.28 (12567) SS BOND : bond 0.00754 / 0.34 ( 3) SS BOND : angle 1.15896 / 0.65 ( 6) hydrogen bonds : bond 0.05601 / 3.60 ( 413) hydrogen bonds : angle 4.22820 / 3.21 ( 1149) Misc. bond : bond 0.00011 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.219 Fit side-chains REVERT: R 255 GLU cc_start: 0.7354 (mp0) cc_final: 0.6968 (mm-30) REVERT: R 290 PHE cc_start: 0.7331 (t80) cc_final: 0.7101 (t80) REVERT: B 59 TYR cc_start: 0.8891 (OUTLIER) cc_final: 0.8363 (m-80) REVERT: B 96 ARG cc_start: 0.8331 (mtp180) cc_final: 0.7650 (mtt180) REVERT: B 197 ARG cc_start: 0.8411 (mtt180) cc_final: 0.7822 (mtp-110) REVERT: B 234 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.8650 (m-80) REVERT: G 20 LYS cc_start: 0.7430 (mttt) cc_final: 0.7034 (mtmt) REVERT: G 21 MET cc_start: 0.5203 (mmt) cc_final: 0.4817 (mmt) REVERT: H 51 MET cc_start: 0.9036 (mmm) cc_final: 0.8810 (mmt) REVERT: A 175 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7437 (tm-30) REVERT: A 220 ASN cc_start: 0.8479 (m-40) cc_final: 0.8229 (m-40) REVERT: A 334 ASP cc_start: 0.8472 (m-30) cc_final: 0.8116 (m-30) outliers start: 24 outliers final: 19 residues processed: 132 average time/residue: 0.0843 time to fit residues: 15.4513 Evaluate side-chains 128 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain R residue 203 CYS Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain R residue 247 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 179 GLN Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 342 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 48 optimal weight: 0.0870 chunk 32 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.165175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.125909 restraints weight = 10322.678| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.03 r_work: 0.3226 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9262 Z= 0.147 Angle : 0.558 8.086 12573 Z= 0.299 Chirality : 0.043 0.164 1395 Planarity : 0.005 0.046 1597 Dihedral : 5.274 82.122 1262 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.07 % Allowed : 10.96 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.24), residues: 1136 helix: 2.33 (0.27), residues: 370 sheet: 1.03 (0.31), residues: 269 loop : -0.45 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.027 0.002 TYR H 207 PHE 0.012 0.001 PHE A 296 TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS H 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 9258) covalent geometry : angle 0.55765 / 0.30 (12567) SS BOND : bond 0.00827 / 0.37 ( 3) SS BOND : angle 1.19765 / 0.65 ( 6) hydrogen bonds : bond 0.06232 / 4.00 ( 413) hydrogen bonds : angle 4.29234 / 3.25 ( 1149) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.202 Fit side-chains REVERT: R 150 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7580 (pt0) REVERT: R 255 GLU cc_start: 0.7456 (mp0) cc_final: 0.7090 (mm-30) REVERT: B 59 TYR cc_start: 0.8908 (OUTLIER) cc_final: 0.8346 (m-80) REVERT: B 96 ARG cc_start: 0.8344 (mtp180) cc_final: 0.7633 (mtt180) REVERT: B 197 ARG cc_start: 0.8440 (mtt180) cc_final: 0.7895 (mtp-110) REVERT: B 234 PHE cc_start: 0.8954 (OUTLIER) cc_final: 0.8673 (m-80) REVERT: G 20 LYS cc_start: 0.7476 (mttt) cc_final: 0.7180 (mtmt) REVERT: G 21 MET cc_start: 0.5339 (mmt) cc_final: 0.4977 (mmt) REVERT: G 42 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6376 (pt0) REVERT: H 68 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8332 (tp) REVERT: H 261 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7573 (ttpt) REVERT: A 175 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7487 (tm-30) REVERT: A 220 ASN cc_start: 0.8490 (m-40) cc_final: 0.8132 (m-40) REVERT: A 334 ASP cc_start: 0.8506 (m-30) cc_final: 0.8180 (m-30) outliers start: 30 outliers final: 23 residues processed: 128 average time/residue: 0.0920 time to fit residues: 16.0780 Evaluate side-chains 134 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 150 GLU Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain R residue 203 CYS Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain R residue 247 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 261 LYS Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 179 GLN Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 342 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 17 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 91 optimal weight: 0.1980 chunk 92 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.168758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.129558 restraints weight = 10372.657| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.03 r_work: 0.3275 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9262 Z= 0.109 Angle : 0.487 7.846 12573 Z= 0.262 Chirality : 0.041 0.152 1395 Planarity : 0.004 0.046 1597 Dihedral : 4.870 69.625 1262 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.87 % Allowed : 11.37 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.25), residues: 1136 helix: 2.54 (0.27), residues: 372 sheet: 1.01 (0.30), residues: 279 loop : -0.38 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 150 TYR 0.020 0.001 TYR H 207 PHE 0.009 0.001 PHE B 151 TRP 0.014 0.001 TRP H 64 HIS 0.003 0.001 HIS H 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 ( 9258) covalent geometry : angle 0.48630 / 0.26 (12567) SS BOND : bond 0.00668 / 0.30 ( 3) SS BOND : angle 1.00747 / 0.56 ( 6) hydrogen bonds : bond 0.04791 / 3.09 ( 413) hydrogen bonds : angle 4.06376 / 3.09 ( 1149) Misc. bond : bond 0.00002 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.289 Fit side-chains REVERT: R 150 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7445 (pt0) REVERT: R 255 GLU cc_start: 0.7380 (mp0) cc_final: 0.7042 (mm-30) REVERT: R 303 MET cc_start: 0.5881 (ttp) cc_final: 0.5326 (tmm) REVERT: B 59 TYR cc_start: 0.8813 (OUTLIER) cc_final: 0.8302 (m-80) REVERT: B 96 ARG cc_start: 0.8288 (mtp180) cc_final: 0.7573 (mtt180) REVERT: B 197 ARG cc_start: 0.8447 (mtt180) cc_final: 0.7794 (mtp-110) REVERT: B 234 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8648 (m-80) REVERT: G 20 LYS cc_start: 0.7469 (mttt) cc_final: 0.7156 (mtmt) REVERT: G 21 MET cc_start: 0.5274 (mmt) cc_final: 0.4904 (mmt) REVERT: H 68 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8168 (tp) REVERT: H 261 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7544 (ttpt) REVERT: A 175 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7525 (tm-30) REVERT: A 220 ASN cc_start: 0.8473 (m-40) cc_final: 0.8143 (m-40) REVERT: A 334 ASP cc_start: 0.8500 (m-30) cc_final: 0.8123 (m-30) outliers start: 28 outliers final: 18 residues processed: 131 average time/residue: 0.0940 time to fit residues: 16.4881 Evaluate side-chains 130 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 150 GLU Chi-restraints excluded: chain R residue 203 CYS Chi-restraints excluded: chain R residue 247 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain H residue 261 LYS Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 179 GLN Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 342 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 16 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 53 optimal weight: 0.0970 chunk 62 optimal weight: 2.9990 chunk 73 optimal weight: 0.0980 chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 72 optimal weight: 0.0060 chunk 83 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 78 optimal weight: 0.0770 overall best weight: 0.1352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.175920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.136683 restraints weight = 10423.678| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.07 r_work: 0.3366 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9262 Z= 0.088 Angle : 0.440 8.221 12573 Z= 0.236 Chirality : 0.040 0.134 1395 Planarity : 0.004 0.046 1597 Dihedral : 4.328 57.337 1262 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.64 % Allowed : 13.11 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.25), residues: 1136 helix: 2.82 (0.27), residues: 372 sheet: 1.14 (0.31), residues: 275 loop : -0.19 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 22 TYR 0.019 0.001 TYR R 118 PHE 0.012 0.001 PHE B 335 TRP 0.014 0.001 TRP B 297 HIS 0.002 0.001 HIS H 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00175 / 0.09 ( 9258) covalent geometry : angle 0.43939 / 0.24 (12567) SS BOND : bond 0.00393 / 0.18 ( 3) SS BOND : angle 0.74403 / 0.42 ( 6) hydrogen bonds : bond 0.03173 / 2.08 ( 413) hydrogen bonds : angle 3.78872 / 2.89 ( 1149) Misc. bond : bond 0.00011 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.334 Fit side-chains REVERT: R 150 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6845 (pt0) REVERT: R 290 PHE cc_start: 0.7294 (t80) cc_final: 0.7074 (t80) REVERT: R 303 MET cc_start: 0.5536 (ttp) cc_final: 0.5172 (tmm) REVERT: B 59 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.8065 (m-80) REVERT: B 78 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8546 (tptt) REVERT: B 96 ARG cc_start: 0.7953 (mtp180) cc_final: 0.7320 (mtt180) REVERT: B 175 GLN cc_start: 0.8468 (mm110) cc_final: 0.8143 (mm-40) REVERT: B 197 ARG cc_start: 0.8208 (mtt180) cc_final: 0.7716 (mtp-110) REVERT: B 234 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.8437 (m-80) REVERT: B 274 THR cc_start: 0.8376 (m) cc_final: 0.8059 (p) REVERT: G 20 LYS cc_start: 0.7387 (mttt) cc_final: 0.7073 (mtmt) REVERT: G 21 MET cc_start: 0.5172 (mmt) cc_final: 0.4837 (mmt) REVERT: A 51 LYS cc_start: 0.6213 (mttt) cc_final: 0.5791 (pttp) REVERT: A 175 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7528 (tm-30) REVERT: A 220 ASN cc_start: 0.8358 (m-40) cc_final: 0.8075 (m-40) REVERT: A 334 ASP cc_start: 0.8249 (m-30) cc_final: 0.7724 (m-30) outliers start: 16 outliers final: 6 residues processed: 133 average time/residue: 0.0870 time to fit residues: 15.6966 Evaluate side-chains 122 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 150 GLU Chi-restraints excluded: chain R residue 247 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 179 GLN Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 342 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 107 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 71 ASN A 28 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.162703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.124431 restraints weight = 10304.460| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.99 r_work: 0.3220 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9262 Z= 0.185 Angle : 0.614 8.683 12573 Z= 0.325 Chirality : 0.045 0.197 1395 Planarity : 0.005 0.046 1597 Dihedral : 5.205 76.127 1262 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.56 % Allowed : 12.19 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.25), residues: 1136 helix: 2.43 (0.27), residues: 371 sheet: 1.08 (0.31), residues: 270 loop : -0.44 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 150 TYR 0.035 0.002 TYR H 207 PHE 0.015 0.002 PHE B 151 TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS H 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 ( 9258) covalent geometry : angle 0.61134 / 0.32 (12567) SS BOND : bond 0.00858 / 0.39 ( 3) SS BOND : angle 2.49911 / 1.40 ( 6) hydrogen bonds : bond 0.06801 / 4.36 ( 413) hydrogen bonds : angle 4.33491 / 3.27 ( 1149) Misc. bond : bond 0.00020 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.263 Fit side-chains REVERT: R 150 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7693 (pt0) REVERT: R 303 MET cc_start: 0.5738 (ttp) cc_final: 0.5338 (tmm) REVERT: B 59 TYR cc_start: 0.8934 (OUTLIER) cc_final: 0.8376 (m-80) REVERT: B 96 ARG cc_start: 0.8317 (mtp180) cc_final: 0.7593 (mtt180) REVERT: B 197 ARG cc_start: 0.8396 (mtt180) cc_final: 0.7782 (mtp-110) REVERT: B 234 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8629 (m-80) REVERT: G 20 LYS cc_start: 0.7540 (mttt) cc_final: 0.7250 (mtmt) REVERT: G 21 MET cc_start: 0.5350 (mmt) cc_final: 0.5007 (mmt) REVERT: H 261 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7575 (ttpt) REVERT: A 175 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7565 (tm-30) REVERT: A 220 ASN cc_start: 0.8466 (m-40) cc_final: 0.8190 (m-40) REVERT: A 334 ASP cc_start: 0.8504 (m-30) cc_final: 0.8193 (m-30) outliers start: 25 outliers final: 18 residues processed: 115 average time/residue: 0.0875 time to fit residues: 13.7142 Evaluate side-chains 117 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 150 GLU Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain R residue 247 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 261 LYS Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 179 GLN Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 342 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 96 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 97 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.167883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.128945 restraints weight = 10308.448| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.03 r_work: 0.3270 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9262 Z= 0.117 Angle : 0.510 8.089 12573 Z= 0.273 Chirality : 0.042 0.183 1395 Planarity : 0.004 0.044 1597 Dihedral : 4.922 67.052 1262 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.15 % Allowed : 12.50 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.25), residues: 1136 helix: 2.56 (0.27), residues: 372 sheet: 1.13 (0.31), residues: 271 loop : -0.40 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 22 TYR 0.022 0.001 TYR H 207 PHE 0.010 0.001 PHE B 151 TRP 0.014 0.001 TRP H 64 HIS 0.004 0.001 HIS H 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 9258) covalent geometry : angle 0.50867 / 0.27 (12567) SS BOND : bond 0.00674 / 0.30 ( 3) SS BOND : angle 1.95995 / 1.09 ( 6) hydrogen bonds : bond 0.05011 / 3.23 ( 413) hydrogen bonds : angle 4.09535 / 3.10 ( 1149) Misc. bond : bond 0.00004 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.277 Fit side-chains REVERT: R 150 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7480 (pt0) REVERT: R 303 MET cc_start: 0.5650 (ttp) cc_final: 0.5406 (tmm) REVERT: B 59 TYR cc_start: 0.8871 (OUTLIER) cc_final: 0.8245 (m-80) REVERT: B 96 ARG cc_start: 0.8269 (mtp180) cc_final: 0.7545 (mtt180) REVERT: B 197 ARG cc_start: 0.8334 (mtt180) cc_final: 0.7741 (mtp-110) REVERT: B 234 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8545 (m-80) REVERT: B 262 MET cc_start: 0.7769 (mtm) cc_final: 0.7554 (mtp) REVERT: G 20 LYS cc_start: 0.7512 (mttt) cc_final: 0.7217 (mtmt) REVERT: G 21 MET cc_start: 0.5302 (mmt) cc_final: 0.4916 (mmt) REVERT: H 261 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7529 (ttpt) REVERT: A 51 LYS cc_start: 0.6074 (mttt) cc_final: 0.5596 (pttp) REVERT: A 175 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7650 (tm-30) REVERT: A 220 ASN cc_start: 0.8449 (m-40) cc_final: 0.8172 (m-40) REVERT: A 334 ASP cc_start: 0.8484 (m-30) cc_final: 0.8116 (m-30) outliers start: 21 outliers final: 15 residues processed: 117 average time/residue: 0.0909 time to fit residues: 14.2638 Evaluate side-chains 120 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 150 GLU Chi-restraints excluded: chain R residue 247 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 261 LYS Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 179 GLN Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 342 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.163933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.125347 restraints weight = 10333.307| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.03 r_work: 0.3223 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9262 Z= 0.171 Angle : 0.597 7.841 12573 Z= 0.316 Chirality : 0.044 0.201 1395 Planarity : 0.005 0.046 1597 Dihedral : 5.275 74.017 1262 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.25 % Allowed : 12.70 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.25), residues: 1136 helix: 2.36 (0.27), residues: 371 sheet: 1.03 (0.31), residues: 270 loop : -0.48 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 150 TYR 0.031 0.002 TYR H 207 PHE 0.023 0.002 PHE R 290 TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS H 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 ( 9258) covalent geometry : angle 0.59536 / 0.32 (12567) SS BOND : bond 0.00905 / 0.41 ( 3) SS BOND : angle 2.05286 / 1.11 ( 6) hydrogen bonds : bond 0.06594 / 4.22 ( 413) hydrogen bonds : angle 4.31475 / 3.26 ( 1149) Misc. bond : bond 0.00016 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.218 Fit side-chains REVERT: R 150 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7632 (pt0) REVERT: R 303 MET cc_start: 0.5847 (ttp) cc_final: 0.5563 (tmm) REVERT: B 59 TYR cc_start: 0.8952 (OUTLIER) cc_final: 0.8377 (m-80) REVERT: B 96 ARG cc_start: 0.8334 (mtp180) cc_final: 0.7621 (mtt180) REVERT: B 197 ARG cc_start: 0.8381 (mtt180) cc_final: 0.7806 (mtp-110) REVERT: B 234 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8614 (m-80) REVERT: B 262 MET cc_start: 0.7870 (mtm) cc_final: 0.7628 (mtp) REVERT: G 20 LYS cc_start: 0.7511 (mttt) cc_final: 0.7218 (mtmt) REVERT: G 21 MET cc_start: 0.5380 (mmt) cc_final: 0.4980 (mmt) REVERT: H 261 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7536 (ttpt) REVERT: A 175 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7555 (tm-30) REVERT: A 220 ASN cc_start: 0.8459 (m-40) cc_final: 0.8181 (m-40) REVERT: A 334 ASP cc_start: 0.8509 (m-30) cc_final: 0.8200 (m-30) outliers start: 22 outliers final: 16 residues processed: 111 average time/residue: 0.0876 time to fit residues: 13.2593 Evaluate side-chains 115 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 150 GLU Chi-restraints excluded: chain R residue 247 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 261 LYS Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 179 GLN Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 342 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 25 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 110 optimal weight: 0.3980 chunk 3 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 69 optimal weight: 0.0030 chunk 50 optimal weight: 4.9990 chunk 12 optimal weight: 0.0970 chunk 109 optimal weight: 2.9990 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.167779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.128819 restraints weight = 10168.974| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.03 r_work: 0.3272 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9262 Z= 0.114 Angle : 0.508 7.384 12573 Z= 0.272 Chirality : 0.041 0.154 1395 Planarity : 0.004 0.044 1597 Dihedral : 4.934 66.579 1262 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.25 % Allowed : 12.70 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.25), residues: 1136 helix: 2.53 (0.27), residues: 372 sheet: 1.04 (0.31), residues: 272 loop : -0.37 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 22 TYR 0.020 0.001 TYR H 207 PHE 0.010 0.001 PHE B 151 TRP 0.014 0.001 TRP H 64 HIS 0.003 0.001 HIS H 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 9258) covalent geometry : angle 0.50634 / 0.27 (12567) SS BOND : bond 0.00746 / 0.34 ( 3) SS BOND : angle 1.77786 / 0.97 ( 6) hydrogen bonds : bond 0.04934 / 3.18 ( 413) hydrogen bonds : angle 4.08980 / 3.10 ( 1149) Misc. bond : bond 0.00004 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2268.79 seconds wall clock time: 39 minutes 18.60 seconds (2358.60 seconds total)