Starting phenix.real_space_refine on Fri Sep 11 04:14:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6oy9_20222/09_2026/6oy9_20222.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oy9_20222/09_2026/6oy9_20222.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6oy9_20222/09_2026/6oy9_20222.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oy9_20222/09_2026/6oy9_20222.map" model { file = "/net/cci-nas-00/data/ceres_data/6oy9_20222/09_2026/6oy9_20222.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oy9_20222/09_2026/6oy9_20222.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6oy9_20222/09_2026/6oy9_20222.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6oy9_20222/09_2026/6oy9_20222.cif" } resolution = 3.9 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= 0.005 sd= 0.436 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 63 5.16 5 C 4810 2.51 5 N 1249 2.21 5 O 1397 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7519 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1809 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 494 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "R" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2589 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 307} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 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: 2.01, per 1000 atoms: 0.27 Number of scatterers: 7519 At special positions: 0 Unit cell: (73.1, 124.7, 122.12, 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 63 16.00 O 1397 8.00 N 1249 7.00 C 4810 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 110 " - pdb=" SG CYS R 187 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 491.4 milliseconds 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1774 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 9 sheets defined 40.0% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 6 through 27 Processing helix chain 'A' and resid 41 through 48 Processing helix chain 'A' and resid 203 through 212 removed outlier: 3.691A pdb=" N LYS A 206 " --> pdb=" O GLU A 203 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TRP A 207 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ILE A 208 " --> pdb=" O LYS A 205 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N HIS A 209 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 251 removed outlier: 3.596A pdb=" N GLU A 241 " --> pdb=" O ASN A 237 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER A 248 " --> pdb=" O HIS A 244 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS A 250 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN A 251 " --> pdb=" O ASN A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 272 through 274 No H-bonds generated for 'chain 'A' and resid 272 through 274' Processing helix chain 'A' and resid 291 through 305 removed outlier: 3.556A pdb=" N ALA A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASN A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 300 " --> pdb=" O GLY A 296 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 336 Processing helix chain 'A' and resid 339 through 348 removed outlier: 3.930A pdb=" N LEU A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS A 345 " --> pdb=" O LYS A 341 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP A 346 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 23 removed outlier: 3.523A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.883A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 26 removed outlier: 4.316A pdb=" N LEU G 15 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LYS G 16 " --> pdb=" O LYS G 12 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 48 removed outlier: 3.957A pdb=" N ARG G 47 " --> pdb=" O TYR G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 51 No H-bonds generated for 'chain 'G' and resid 49 through 51' Processing helix chain 'R' and resid 33 through 65 removed outlier: 3.561A pdb=" N PHE R 37 " --> pdb=" O GLU R 33 " (cutoff:3.500A) Proline residue: R 53 - end of helix removed outlier: 3.973A pdb=" N HIS R 65 " --> pdb=" O VAL R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 89 removed outlier: 3.687A pdb=" N ASP R 83 " --> pdb=" O LEU R 79 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU R 84 " --> pdb=" O ALA R 80 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE R 85 " --> pdb=" O VAL R 81 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET R 86 " --> pdb=" O ALA R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 100 Processing helix chain 'R' and resid 106 through 141 removed outlier: 4.139A pdb=" N PHE R 115 " --> pdb=" O ASN R 111 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY R 120 " --> pdb=" O PHE R 116 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY R 121 " --> pdb=" O ALA R 117 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS R 141 " --> pdb=" O VAL R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 167 Processing helix chain 'R' and resid 195 through 198 removed outlier: 3.666A pdb=" N THR R 198 " --> pdb=" O HIS R 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 195 through 198' Processing helix chain 'R' and resid 199 through 211 removed outlier: 3.666A pdb=" N PHE R 203 " --> pdb=" O ASN R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 235 Processing helix chain 'R' and resid 240 through 266 removed outlier: 3.724A pdb=" N GLN R 244 " --> pdb=" O SER R 240 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS R 248 " --> pdb=" O GLN R 244 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE R 255 " --> pdb=" O THR R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 278 Processing helix chain 'R' and resid 286 through 288 No H-bonds generated for 'chain 'R' and resid 286 through 288' Processing helix chain 'R' and resid 289 through 297 Processing helix chain 'R' and resid 298 through 300 No H-bonds generated for 'chain 'R' and resid 298 through 300' Processing helix chain 'R' and resid 313 through 318 Processing sheet with id=AA1, first strand: chain 'A' and resid 192 through 195 removed outlier: 3.570A pdb=" N ARG A 193 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 34 " --> pdb=" O PHE A 195 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE A 218 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU A 33 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE A 217 " --> pdb=" O ILE A 261 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 50 removed outlier: 4.110A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY B 319 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.154A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N MET B 61 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 81 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 104 Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.878A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER B 160 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.989A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.384A 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: 3.611A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.372A 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: 7.117A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 4 through 5 286 hydrogen bonds defined for protein. 825 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: 1.07 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2300 1.34 - 1.45: 1462 1.45 - 1.57: 3827 1.57 - 1.69: 0 1.69 - 1.81: 94 Bond restraints: 7683 Sorted by residual: bond pdb=" C7 RET R 401 " pdb=" C8 RET R 401 " ideal model delta sigma weight residual 1.349 1.298 0.051 2.00e-02 2.50e+03 6.44e+00 bond pdb=" CA LEU B 336 " pdb=" CB LEU B 336 " ideal model delta sigma weight residual 1.525 1.492 0.033 1.47e-02 4.63e+03 5.06e+00 bond pdb=" CB PHE B 234 " pdb=" CG PHE B 234 " ideal model delta sigma weight residual 1.502 1.451 0.051 2.30e-02 1.89e+03 4.95e+00 bond pdb=" CB TRP B 99 " pdb=" CG TRP B 99 " ideal model delta sigma weight residual 1.498 1.431 0.067 3.10e-02 1.04e+03 4.61e+00 bond pdb=" C PHE B 199 " pdb=" N VAL B 200 " ideal model delta sigma weight residual 1.327 1.269 0.058 2.97e-02 1.13e+03 3.84e+00 ... (remaining 7678 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.49: 10216 3.49 - 6.98: 159 6.98 - 10.47: 16 10.47 - 13.96: 3 13.96 - 17.45: 1 Bond angle restraints: 10395 Sorted by residual: angle pdb=" CA LEU G 32 " pdb=" CB LEU G 32 " pdb=" CG LEU G 32 " ideal model delta sigma weight residual 116.30 133.75 -17.45 3.50e+00 8.16e-02 2.48e+01 angle pdb=" C VAL R 300 " pdb=" N TYR R 301 " pdb=" CA TYR R 301 " ideal model delta sigma weight residual 122.38 114.17 8.21 1.81e+00 3.05e-01 2.06e+01 angle pdb=" C GLU R 25 " pdb=" N ALA R 26 " pdb=" CA ALA R 26 " ideal model delta sigma weight residual 121.80 132.53 -10.73 2.44e+00 1.68e-01 1.93e+01 angle pdb=" CA PRO R 291 " pdb=" N PRO R 291 " pdb=" CD PRO R 291 " ideal model delta sigma weight residual 112.00 106.52 5.48 1.40e+00 5.10e-01 1.53e+01 angle pdb=" C CYS R 322 " pdb=" N CYS R 323 " pdb=" CA CYS R 323 " ideal model delta sigma weight residual 122.08 127.41 -5.33 1.47e+00 4.63e-01 1.31e+01 ... (remaining 10390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 3915 16.99 - 33.98: 526 33.98 - 50.98: 95 50.98 - 67.97: 13 67.97 - 84.96: 5 Dihedral angle restraints: 4554 sinusoidal: 1805 harmonic: 2749 Sorted by residual: dihedral pdb=" CB CYS R 110 " pdb=" SG CYS R 110 " pdb=" SG CYS R 187 " pdb=" CB CYS R 187 " ideal model delta sinusoidal sigma weight residual -86.00 -139.86 53.86 1 1.00e+01 1.00e-02 3.94e+01 dihedral pdb=" CA LYS A 275 " pdb=" C LYS A 275 " pdb=" N LYS A 276 " pdb=" CA LYS A 276 " ideal model delta harmonic sigma weight residual -180.00 -153.10 -26.90 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA ASP B 118 " pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta harmonic sigma weight residual -180.00 -154.61 -25.39 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 4551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1050 0.112 - 0.224: 105 0.224 - 0.336: 1 0.336 - 0.448: 0 0.448 - 0.561: 1 Chirality restraints: 1157 Sorted by residual: chirality pdb=" CB ILE R 214 " pdb=" CA ILE R 214 " pdb=" CG1 ILE R 214 " pdb=" CG2 ILE R 214 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.56 2.00e-01 2.50e+01 7.86e+00 chirality pdb=" CB VAL B 320 " pdb=" CA VAL B 320 " pdb=" CG1 VAL B 320 " pdb=" CG2 VAL B 320 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB ILE B 43 " pdb=" CA ILE B 43 " pdb=" CG1 ILE B 43 " pdb=" CG2 ILE B 43 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1154 not shown) Planarity restraints: 1326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 70 " 0.072 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO R 71 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO R 71 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO R 71 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO R 170 " 0.068 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO R 171 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO R 171 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO R 171 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 82 " 0.021 2.00e-02 2.50e+03 2.05e-02 1.06e+01 pdb=" CG TRP B 82 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP B 82 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP B 82 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP B 82 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 82 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 82 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 82 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 82 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 82 " -0.002 2.00e-02 2.50e+03 ... (remaining 1323 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2147 2.80 - 3.32: 6890 3.32 - 3.85: 11894 3.85 - 4.37: 12456 4.37 - 4.90: 21424 Nonbonded interactions: 54811 Sorted by model distance: nonbonded pdb=" O SER B 84 " pdb=" OG SER B 84 " model vdw 2.269 3.040 nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 334 " model vdw 2.284 3.040 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.291 3.040 nonbonded pdb=" OG SER R 22 " pdb=" OE1 GLU R 25 " model vdw 2.302 3.040 nonbonded pdb=" O SER R 298 " pdb=" OG SER R 298 " model vdw 2.304 3.040 ... (remaining 54806 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 8.890 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.138 7685 Z= 0.436 Angle : 1.097 17.446 10397 Z= 0.589 Chirality : 0.065 0.561 1157 Planarity : 0.008 0.108 1326 Dihedral : 15.304 84.962 2777 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 0.24 % Allowed : 17.56 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.69 (0.21), residues: 938 helix: -2.38 (0.22), residues: 348 sheet: -3.07 (0.36), residues: 135 loop : -3.78 (0.21), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 30 TYR 0.038 0.004 TYR R 96 PHE 0.022 0.003 PHE B 241 TRP 0.054 0.004 TRP B 82 HIS 0.009 0.002 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00917 / 0.41 ( 7683) covalent geometry : angle 1.09717 / 0.59 (10395) SS BOND : bond 0.00148 / 0.08 ( 1) SS BOND : angle 0.22454 / 0.13 ( 2) hydrogen bonds : bond 0.15729 / 10.58 ( 286) hydrogen bonds : angle 6.00769 / 4.05 ( 825) Misc. bond : bond 0.13822 / 7.27 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 152 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8678 (ptp-170) cc_final: 0.8397 (ptp90) REVERT: A 49 MET cc_start: 0.8944 (tpp) cc_final: 0.8415 (mmm) REVERT: A 193 ARG cc_start: 0.8934 (ttm110) cc_final: 0.8649 (mtp85) REVERT: A 238 ARG cc_start: 0.8755 (ttm170) cc_final: 0.8474 (ttp-170) REVERT: A 306 LEU cc_start: 0.9248 (tp) cc_final: 0.8920 (tp) REVERT: B 215 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7994 (mm-30) REVERT: B 260 GLU cc_start: 0.8122 (mp0) cc_final: 0.7887 (mp0) REVERT: B 271 CYS cc_start: 0.7359 (p) cc_final: 0.6616 (p) REVERT: B 290 ASP cc_start: 0.7761 (m-30) cc_final: 0.7186 (m-30) REVERT: B 325 MET cc_start: 0.8172 (mmt) cc_final: 0.7877 (mmm) REVERT: G 12 LYS cc_start: 0.7789 (mttt) cc_final: 0.7407 (mmmt) REVERT: R 44 MET cc_start: 0.8920 (tpp) cc_final: 0.8666 (tpp) REVERT: R 69 ARG cc_start: 0.8324 (ttp-170) cc_final: 0.7844 (ttm-80) REVERT: R 179 ILE cc_start: 0.8710 (mt) cc_final: 0.8494 (tp) REVERT: R 190 ASP cc_start: 0.7536 (p0) cc_final: 0.7011 (p0) REVERT: R 200 ASN cc_start: 0.7986 (t0) cc_final: 0.6630 (t0) REVERT: R 231 LYS cc_start: 0.8897 (tppt) cc_final: 0.8596 (tmtt) outliers start: 2 outliers final: 2 residues processed: 154 average time/residue: 0.1012 time to fit residues: 20.4581 Evaluate side-chains 116 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 176 SER Chi-restraints excluded: chain R residue 198 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 GLN B 293 ASN B 311 HIS R 100 HIS R 238 GLN R 278 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.114219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.089704 restraints weight = 16086.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.092505 restraints weight = 9087.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.094401 restraints weight = 6299.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.095653 restraints weight = 4945.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.096363 restraints weight = 4220.136| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7685 Z= 0.126 Angle : 0.667 15.076 10397 Z= 0.343 Chirality : 0.042 0.250 1157 Planarity : 0.005 0.083 1326 Dihedral : 6.028 44.078 1027 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.44 % Allowed : 20.37 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.25), residues: 938 helix: -0.45 (0.27), residues: 352 sheet: -2.40 (0.40), residues: 139 loop : -3.36 (0.24), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 309 TYR 0.028 0.002 TYR R 96 PHE 0.026 0.001 PHE B 235 TRP 0.021 0.002 TRP R 35 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 7683) covalent geometry : angle 0.66718 / 0.34 (10395) SS BOND : bond 0.00136 / 0.07 ( 1) SS BOND : angle 0.29951 / 0.17 ( 2) hydrogen bonds : bond 0.04776 / 3.23 ( 286) hydrogen bonds : angle 4.57592 / 3.06 ( 825) Misc. bond : bond 0.00011 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8634 (ptp-170) cc_final: 0.8419 (ptp90) REVERT: A 194 MET cc_start: 0.9039 (ptp) cc_final: 0.8837 (ptp) REVERT: A 238 ARG cc_start: 0.8705 (ttm170) cc_final: 0.8063 (mmp-170) REVERT: A 306 LEU cc_start: 0.9118 (tp) cc_final: 0.8748 (tp) REVERT: B 10 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8104 (mp0) REVERT: B 215 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7983 (mm-30) REVERT: B 262 MET cc_start: 0.8395 (tpt) cc_final: 0.8013 (tpp) REVERT: B 264 TYR cc_start: 0.8618 (m-80) cc_final: 0.8334 (m-80) REVERT: B 271 CYS cc_start: 0.6710 (p) cc_final: 0.6016 (p) REVERT: B 290 ASP cc_start: 0.7449 (m-30) cc_final: 0.6922 (m-30) REVERT: G 12 LYS cc_start: 0.7624 (mttt) cc_final: 0.7265 (mmmt) REVERT: R 44 MET cc_start: 0.8880 (tpp) cc_final: 0.8642 (tpp) REVERT: R 68 LEU cc_start: 0.8894 (tt) cc_final: 0.8655 (mp) REVERT: R 69 ARG cc_start: 0.8164 (ttp-170) cc_final: 0.7640 (ttm-80) REVERT: R 145 ASN cc_start: 0.8446 (t0) cc_final: 0.8208 (t0) REVERT: R 176 SER cc_start: 0.9222 (p) cc_final: 0.8832 (m) outliers start: 20 outliers final: 5 residues processed: 173 average time/residue: 0.0933 time to fit residues: 21.4151 Evaluate side-chains 131 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 126 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain R residue 290 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 87 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 9 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 55.4892 > 50:) chunk 19 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 HIS ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 340 ASN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 28 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.121601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.096344 restraints weight = 14996.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.099177 restraints weight = 8562.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.101005 restraints weight = 5981.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.102395 restraints weight = 4748.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.103016 restraints weight = 4041.170| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7685 Z= 0.142 Angle : 0.662 12.942 10397 Z= 0.339 Chirality : 0.043 0.266 1157 Planarity : 0.005 0.083 1326 Dihedral : 5.526 39.344 1025 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 3.05 % Allowed : 23.78 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.27), residues: 938 helix: 0.41 (0.29), residues: 353 sheet: -2.02 (0.44), residues: 137 loop : -3.19 (0.25), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.025 0.002 TYR R 96 PHE 0.020 0.001 PHE B 235 TRP 0.018 0.002 TRP B 339 HIS 0.006 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 7683) covalent geometry : angle 0.66187 / 0.34 (10395) SS BOND : bond 0.00088 / 0.05 ( 1) SS BOND : angle 0.27891 / 0.15 ( 2) hydrogen bonds : bond 0.04583 / 3.12 ( 286) hydrogen bonds : angle 4.33796 / 2.93 ( 825) Misc. bond : bond 0.00029 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7667 (mttt) cc_final: 0.6761 (tmtt) REVERT: A 28 ARG cc_start: 0.8562 (ptp-170) cc_final: 0.8325 (ptp90) REVERT: A 238 ARG cc_start: 0.8498 (ttm170) cc_final: 0.8040 (mmp-170) REVERT: A 306 LEU cc_start: 0.9092 (tp) cc_final: 0.8597 (tt) REVERT: B 215 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7934 (mm-30) REVERT: B 260 GLU cc_start: 0.8007 (mp0) cc_final: 0.7804 (mp0) REVERT: G 12 LYS cc_start: 0.7572 (mttt) cc_final: 0.7231 (mmmt) REVERT: R 44 MET cc_start: 0.8906 (tpp) cc_final: 0.8690 (tpp) REVERT: R 69 ARG cc_start: 0.8040 (ttp-170) cc_final: 0.7732 (ttm-80) REVERT: R 183 MET cc_start: 0.8660 (mmt) cc_final: 0.8390 (mmt) REVERT: R 190 ASP cc_start: 0.7606 (p0) cc_final: 0.7325 (p0) REVERT: R 201 GLU cc_start: 0.7718 (tp30) cc_final: 0.7384 (tp30) REVERT: R 231 LYS cc_start: 0.8915 (ttmt) cc_final: 0.8686 (ttmm) outliers start: 25 outliers final: 11 residues processed: 159 average time/residue: 0.0882 time to fit residues: 18.9447 Evaluate side-chains 140 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 304 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 80 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.124260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.099016 restraints weight = 15187.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.101953 restraints weight = 8551.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.103958 restraints weight = 5935.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.105303 restraints weight = 4664.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.105919 restraints weight = 3970.631| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7685 Z= 0.115 Angle : 0.642 12.278 10397 Z= 0.321 Chirality : 0.042 0.269 1157 Planarity : 0.004 0.075 1326 Dihedral : 5.158 36.346 1025 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.17 % Allowed : 25.49 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.28), residues: 938 helix: 0.79 (0.29), residues: 354 sheet: -1.99 (0.43), residues: 144 loop : -3.00 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 193 TYR 0.022 0.001 TYR R 96 PHE 0.015 0.001 PHE B 235 TRP 0.021 0.002 TRP B 339 HIS 0.003 0.000 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 7683) covalent geometry : angle 0.64157 / 0.32 (10395) SS BOND : bond 0.00063 / 0.03 ( 1) SS BOND : angle 0.34103 / 0.20 ( 2) hydrogen bonds : bond 0.03916 / 2.65 ( 286) hydrogen bonds : angle 4.17933 / 2.81 ( 825) Misc. bond : bond 0.00018 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7644 (mttt) cc_final: 0.6790 (tmtt) REVERT: A 238 ARG cc_start: 0.8378 (ttm170) cc_final: 0.8141 (mmp-170) REVERT: A 342 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7744 (tm-30) REVERT: B 215 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7916 (mm-30) REVERT: B 262 MET cc_start: 0.8501 (tpt) cc_final: 0.7908 (tpp) REVERT: G 12 LYS cc_start: 0.7434 (mttt) cc_final: 0.7148 (mmmt) REVERT: G 20 ASP cc_start: 0.8122 (m-30) cc_final: 0.7368 (p0) REVERT: R 44 MET cc_start: 0.8909 (tpp) cc_final: 0.8686 (tpp) REVERT: R 69 ARG cc_start: 0.7938 (ttp-170) cc_final: 0.7527 (ttm-80) REVERT: R 176 SER cc_start: 0.8986 (p) cc_final: 0.8600 (m) REVERT: R 190 ASP cc_start: 0.7363 (p0) cc_final: 0.7077 (p0) REVERT: R 201 GLU cc_start: 0.7668 (tp30) cc_final: 0.7252 (tp30) REVERT: R 231 LYS cc_start: 0.8898 (ttmt) cc_final: 0.8667 (ttmm) outliers start: 26 outliers final: 15 residues processed: 161 average time/residue: 0.0912 time to fit residues: 19.7961 Evaluate side-chains 143 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 85 PHE Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 304 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 15 optimal weight: 0.0020 chunk 88 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 119 ASN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.125385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.100174 restraints weight = 15196.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.103170 restraints weight = 8582.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.105213 restraints weight = 5940.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.106546 restraints weight = 4661.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.107372 restraints weight = 3976.555| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7685 Z= 0.109 Angle : 0.625 13.279 10397 Z= 0.312 Chirality : 0.042 0.263 1157 Planarity : 0.004 0.075 1326 Dihedral : 4.933 34.810 1025 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.44 % Allowed : 27.07 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.28), residues: 938 helix: 1.04 (0.30), residues: 354 sheet: -1.73 (0.44), residues: 142 loop : -2.88 (0.26), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 96 TYR 0.018 0.001 TYR R 96 PHE 0.014 0.001 PHE B 235 TRP 0.019 0.001 TRP B 82 HIS 0.003 0.000 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 7683) covalent geometry : angle 0.62504 / 0.31 (10395) SS BOND : bond 0.00053 / 0.03 ( 1) SS BOND : angle 0.20083 / 0.12 ( 2) hydrogen bonds : bond 0.03575 / 2.41 ( 286) hydrogen bonds : angle 4.03375 / 2.70 ( 825) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7637 (mttt) cc_final: 0.6846 (tmtt) REVERT: A 342 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7703 (tm-30) REVERT: B 183 HIS cc_start: 0.8253 (OUTLIER) cc_final: 0.7977 (t-90) REVERT: B 221 THR cc_start: 0.7642 (OUTLIER) cc_final: 0.7310 (p) REVERT: B 262 MET cc_start: 0.8368 (tpt) cc_final: 0.7814 (tpp) REVERT: B 278 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7638 (m-10) REVERT: R 44 MET cc_start: 0.8895 (tpp) cc_final: 0.8674 (tpp) REVERT: R 113 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8404 (tm-30) REVERT: R 127 SER cc_start: 0.8442 (m) cc_final: 0.8140 (p) REVERT: R 176 SER cc_start: 0.9035 (p) cc_final: 0.8715 (m) REVERT: R 183 MET cc_start: 0.8758 (mmt) cc_final: 0.8522 (mmt) REVERT: R 190 ASP cc_start: 0.7301 (p0) cc_final: 0.6911 (p0) REVERT: R 201 GLU cc_start: 0.7600 (tp30) cc_final: 0.7126 (tp30) REVERT: R 231 LYS cc_start: 0.8891 (ttmt) cc_final: 0.8652 (ttmm) outliers start: 20 outliers final: 14 residues processed: 156 average time/residue: 0.0898 time to fit residues: 18.9747 Evaluate side-chains 150 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 292 TYR Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 297 THR Chi-restraints excluded: chain R residue 304 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 13 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 ASN G 21 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.125334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.097877 restraints weight = 15248.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.100827 restraints weight = 8830.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.102844 restraints weight = 6261.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.103980 restraints weight = 5006.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.105083 restraints weight = 4365.588| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7685 Z= 0.135 Angle : 0.641 11.899 10397 Z= 0.321 Chirality : 0.043 0.267 1157 Planarity : 0.004 0.073 1326 Dihedral : 4.901 32.172 1025 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.29 % Allowed : 26.83 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.53 (0.28), residues: 938 helix: 1.23 (0.30), residues: 347 sheet: -1.43 (0.46), residues: 134 loop : -2.83 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 41 TYR 0.023 0.002 TYR B 111 PHE 0.027 0.001 PHE B 199 TRP 0.015 0.002 TRP B 339 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 7683) covalent geometry : angle 0.64153 / 0.32 (10395) SS BOND : bond 0.00100 / 0.05 ( 1) SS BOND : angle 0.28331 / 0.16 ( 2) hydrogen bonds : bond 0.03950 / 2.69 ( 286) hydrogen bonds : angle 4.07430 / 2.73 ( 825) Misc. bond : bond 0.00022 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.256 Fit side-chains REVERT: A 10 LYS cc_start: 0.7667 (mttt) cc_final: 0.6849 (tmtt) REVERT: A 238 ARG cc_start: 0.8422 (mmp-170) cc_final: 0.8006 (mmm-85) REVERT: A 239 MET cc_start: 0.7865 (tmm) cc_final: 0.7096 (mmm) REVERT: A 342 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7751 (tm-30) REVERT: B 153 ASP cc_start: 0.7954 (p0) cc_final: 0.7621 (p0) REVERT: B 262 MET cc_start: 0.8451 (tpt) cc_final: 0.7895 (tpp) REVERT: B 264 TYR cc_start: 0.8282 (m-80) cc_final: 0.8049 (m-80) REVERT: B 278 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.7628 (m-10) REVERT: B 325 MET cc_start: 0.8057 (mmt) cc_final: 0.7577 (tpp) REVERT: G 12 LYS cc_start: 0.7378 (mmtp) cc_final: 0.7079 (mmmt) REVERT: G 20 ASP cc_start: 0.8187 (m-30) cc_final: 0.7383 (p0) REVERT: R 44 MET cc_start: 0.8882 (tpp) cc_final: 0.8674 (tpp) REVERT: R 76 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8489 (tt) REVERT: R 176 SER cc_start: 0.9021 (p) cc_final: 0.8691 (m) REVERT: R 183 MET cc_start: 0.8824 (mmt) cc_final: 0.8547 (mmt) REVERT: R 190 ASP cc_start: 0.7394 (p0) cc_final: 0.7061 (p0) REVERT: R 201 GLU cc_start: 0.7631 (tp30) cc_final: 0.7192 (tp30) REVERT: R 231 LYS cc_start: 0.8929 (ttmt) cc_final: 0.8684 (ttmm) REVERT: R 253 MET cc_start: 0.8806 (tpp) cc_final: 0.8493 (tpp) REVERT: R 311 LYS cc_start: 0.9030 (tppp) cc_final: 0.8803 (tppp) outliers start: 27 outliers final: 18 residues processed: 154 average time/residue: 0.0816 time to fit residues: 17.2176 Evaluate side-chains 145 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 292 TYR Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 21 GLN Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 297 THR Chi-restraints excluded: chain R residue 304 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 25 optimal weight: 50.0000 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 63 optimal weight: 0.3980 chunk 76 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 39 optimal weight: 0.0270 chunk 6 optimal weight: 5.9990 overall best weight: 0.8642 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.129010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.102927 restraints weight = 14823.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.106067 restraints weight = 8248.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.108092 restraints weight = 5664.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.109655 restraints weight = 4455.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.110444 restraints weight = 3772.281| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7685 Z= 0.105 Angle : 0.620 11.274 10397 Z= 0.309 Chirality : 0.041 0.269 1157 Planarity : 0.004 0.075 1326 Dihedral : 4.759 34.513 1025 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.17 % Allowed : 27.20 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.28), residues: 938 helix: 1.39 (0.30), residues: 347 sheet: -1.19 (0.47), residues: 135 loop : -2.73 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 96 TYR 0.021 0.001 TYR B 111 PHE 0.025 0.001 PHE B 199 TRP 0.011 0.001 TRP R 35 HIS 0.003 0.000 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 ( 7683) covalent geometry : angle 0.62014 / 0.31 (10395) SS BOND : bond 0.00067 / 0.04 ( 1) SS BOND : angle 0.12028 / 0.07 ( 2) hydrogen bonds : bond 0.03375 / 2.28 ( 286) hydrogen bonds : angle 4.01382 / 2.69 ( 825) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7745 (mttt) cc_final: 0.6921 (tmtt) REVERT: A 239 MET cc_start: 0.7924 (tmm) cc_final: 0.7536 (tmm) REVERT: A 342 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7721 (tm-30) REVERT: B 153 ASP cc_start: 0.7887 (p0) cc_final: 0.7503 (p0) REVERT: B 183 HIS cc_start: 0.8265 (OUTLIER) cc_final: 0.8016 (t-90) REVERT: B 262 MET cc_start: 0.8447 (tpt) cc_final: 0.7857 (tpp) REVERT: B 264 TYR cc_start: 0.8198 (m-80) cc_final: 0.7926 (m-80) REVERT: B 278 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.7610 (m-10) REVERT: B 325 MET cc_start: 0.8057 (mmt) cc_final: 0.7651 (tpp) REVERT: G 12 LYS cc_start: 0.7328 (mmtp) cc_final: 0.7075 (mmmt) REVERT: G 32 LEU cc_start: 0.8184 (pt) cc_final: 0.7902 (pp) REVERT: G 36 CYS cc_start: 0.7479 (OUTLIER) cc_final: 0.7089 (p) REVERT: G 51 ASP cc_start: 0.9184 (t70) cc_final: 0.8900 (t0) REVERT: R 44 MET cc_start: 0.8854 (tpp) cc_final: 0.8641 (tpp) REVERT: R 113 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8391 (tm-30) REVERT: R 127 SER cc_start: 0.8519 (m) cc_final: 0.8298 (p) REVERT: R 176 SER cc_start: 0.9001 (p) cc_final: 0.8655 (m) REVERT: R 183 MET cc_start: 0.8795 (mmt) cc_final: 0.8421 (mmp) REVERT: R 190 ASP cc_start: 0.7279 (p0) cc_final: 0.7038 (p0) REVERT: R 201 GLU cc_start: 0.7480 (tp30) cc_final: 0.6988 (tp30) REVERT: R 231 LYS cc_start: 0.8893 (ttmt) cc_final: 0.8650 (ttmm) REVERT: R 253 MET cc_start: 0.8775 (tpp) cc_final: 0.8488 (tpp) REVERT: R 286 ILE cc_start: 0.8614 (tt) cc_final: 0.8267 (mm) outliers start: 26 outliers final: 17 residues processed: 164 average time/residue: 0.0845 time to fit residues: 19.0166 Evaluate side-chains 159 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 297 THR Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 309 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 34 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 22 optimal weight: 0.0030 chunk 90 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 49 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 42 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.129767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.103398 restraints weight = 14872.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.106554 restraints weight = 8282.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.108646 restraints weight = 5709.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.110121 restraints weight = 4494.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.111023 restraints weight = 3816.775| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7685 Z= 0.108 Angle : 0.623 10.858 10397 Z= 0.310 Chirality : 0.041 0.259 1157 Planarity : 0.004 0.075 1326 Dihedral : 4.587 34.154 1025 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.80 % Allowed : 27.68 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.28), residues: 938 helix: 1.46 (0.30), residues: 347 sheet: -1.09 (0.47), residues: 135 loop : -2.65 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 193 TYR 0.021 0.001 TYR B 111 PHE 0.023 0.001 PHE B 199 TRP 0.011 0.001 TRP B 297 HIS 0.003 0.000 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 7683) covalent geometry : angle 0.62261 / 0.31 (10395) SS BOND : bond 0.00019 / 0.01 ( 1) SS BOND : angle 0.14163 / 0.08 ( 2) hydrogen bonds : bond 0.03334 / 2.26 ( 286) hydrogen bonds : angle 3.96905 / 2.66 ( 825) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.286 Fit side-chains REVERT: A 10 LYS cc_start: 0.7717 (mttt) cc_final: 0.6929 (tmtt) REVERT: A 239 MET cc_start: 0.7938 (tmm) cc_final: 0.7411 (tmm) REVERT: A 342 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7655 (tm-30) REVERT: B 82 TRP cc_start: 0.8742 (OUTLIER) cc_final: 0.8536 (p90) REVERT: B 153 ASP cc_start: 0.7936 (p0) cc_final: 0.7614 (p0) REVERT: B 262 MET cc_start: 0.8477 (tpt) cc_final: 0.7880 (tpp) REVERT: B 264 TYR cc_start: 0.8222 (m-80) cc_final: 0.7891 (m-80) REVERT: B 278 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7663 (m-10) REVERT: B 325 MET cc_start: 0.7997 (mmt) cc_final: 0.7710 (tpp) REVERT: G 12 LYS cc_start: 0.7209 (mmtp) cc_final: 0.6997 (mmmt) REVERT: G 20 ASP cc_start: 0.8201 (m-30) cc_final: 0.7392 (p0) REVERT: G 32 LEU cc_start: 0.8162 (pt) cc_final: 0.7852 (pp) REVERT: G 36 CYS cc_start: 0.7436 (OUTLIER) cc_final: 0.7071 (p) REVERT: R 44 MET cc_start: 0.8847 (tpp) cc_final: 0.8628 (tpp) REVERT: R 113 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8350 (tm-30) REVERT: R 176 SER cc_start: 0.9011 (p) cc_final: 0.8653 (m) REVERT: R 183 MET cc_start: 0.8817 (mmt) cc_final: 0.8439 (mmp) REVERT: R 190 ASP cc_start: 0.7440 (p0) cc_final: 0.7048 (p0) REVERT: R 201 GLU cc_start: 0.7421 (tp30) cc_final: 0.6901 (tp30) REVERT: R 231 LYS cc_start: 0.8905 (ttmt) cc_final: 0.8660 (ttmm) REVERT: R 253 MET cc_start: 0.8719 (tpp) cc_final: 0.8498 (tpp) REVERT: R 286 ILE cc_start: 0.8607 (tt) cc_final: 0.8258 (mm) outliers start: 23 outliers final: 18 residues processed: 156 average time/residue: 0.0870 time to fit residues: 18.5501 Evaluate side-chains 154 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 292 TYR Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 297 THR Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 309 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 57 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 49 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 HIS B 183 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 145 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.126167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.099554 restraints weight = 14999.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.102584 restraints weight = 8382.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.104642 restraints weight = 5819.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.106004 restraints weight = 4582.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.106757 restraints weight = 3933.350| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7685 Z= 0.156 Angle : 0.681 12.288 10397 Z= 0.341 Chirality : 0.043 0.274 1157 Planarity : 0.004 0.074 1326 Dihedral : 4.781 32.171 1025 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.68 % Allowed : 28.29 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.28), residues: 938 helix: 1.43 (0.30), residues: 348 sheet: -1.14 (0.50), residues: 123 loop : -2.62 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 193 TYR 0.022 0.002 TYR B 111 PHE 0.019 0.001 PHE B 199 TRP 0.017 0.001 TRP R 35 HIS 0.005 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 7683) covalent geometry : angle 0.68121 / 0.34 (10395) SS BOND : bond 0.00059 / 0.03 ( 1) SS BOND : angle 0.20644 / 0.11 ( 2) hydrogen bonds : bond 0.04114 / 2.79 ( 286) hydrogen bonds : angle 4.08975 / 2.75 ( 825) Misc. bond : bond 0.00021 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.304 Fit side-chains REVERT: A 10 LYS cc_start: 0.7700 (mttt) cc_final: 0.6860 (tmtt) REVERT: A 28 ARG cc_start: 0.8470 (ttp-110) cc_final: 0.8230 (ttm110) REVERT: A 239 MET cc_start: 0.7968 (tmm) cc_final: 0.7252 (mmm) REVERT: A 342 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7741 (tm-30) REVERT: B 82 TRP cc_start: 0.8801 (OUTLIER) cc_final: 0.8454 (p90) REVERT: B 262 MET cc_start: 0.8499 (tpt) cc_final: 0.7840 (tpp) REVERT: B 264 TYR cc_start: 0.8349 (m-80) cc_final: 0.8087 (m-80) REVERT: B 278 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7557 (m-10) REVERT: B 325 MET cc_start: 0.8169 (mmt) cc_final: 0.7569 (tpp) REVERT: G 20 ASP cc_start: 0.8235 (m-30) cc_final: 0.7448 (p0) REVERT: G 32 LEU cc_start: 0.8185 (pt) cc_final: 0.7943 (pp) REVERT: G 36 CYS cc_start: 0.7421 (OUTLIER) cc_final: 0.7069 (p) REVERT: R 44 MET cc_start: 0.8920 (tpp) cc_final: 0.8692 (tpp) REVERT: R 176 SER cc_start: 0.9049 (p) cc_final: 0.8717 (m) REVERT: R 183 MET cc_start: 0.8903 (mmt) cc_final: 0.8202 (mmp) REVERT: R 190 ASP cc_start: 0.7578 (p0) cc_final: 0.7284 (p0) REVERT: R 201 GLU cc_start: 0.7587 (tp30) cc_final: 0.7139 (tp30) REVERT: R 231 LYS cc_start: 0.8941 (ttmt) cc_final: 0.8711 (ttmm) REVERT: R 253 MET cc_start: 0.8802 (tpp) cc_final: 0.8539 (tpp) outliers start: 22 outliers final: 17 residues processed: 146 average time/residue: 0.0885 time to fit residues: 17.5745 Evaluate side-chains 148 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 292 TYR Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 145 ASN Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 297 THR Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 309 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 63 optimal weight: 0.0980 chunk 16 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 89 optimal weight: 0.0070 chunk 11 optimal weight: 6.9990 chunk 55 optimal weight: 0.1980 chunk 41 optimal weight: 0.0770 chunk 72 optimal weight: 0.9990 overall best weight: 0.2758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 145 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.130545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.105503 restraints weight = 14699.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.108523 restraints weight = 8383.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.110575 restraints weight = 5838.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.111994 restraints weight = 4589.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.112745 restraints weight = 3902.869| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7685 Z= 0.113 Angle : 0.674 12.419 10397 Z= 0.329 Chirality : 0.041 0.254 1157 Planarity : 0.004 0.076 1326 Dihedral : 4.584 35.043 1025 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.20 % Allowed : 29.27 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.28), residues: 938 helix: 1.49 (0.30), residues: 349 sheet: -1.08 (0.48), residues: 137 loop : -2.53 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 193 TYR 0.021 0.001 TYR B 111 PHE 0.023 0.001 PHE B 199 TRP 0.013 0.001 TRP B 297 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 7683) covalent geometry : angle 0.67438 / 0.33 (10395) SS BOND : bond 0.00034 / 0.02 ( 1) SS BOND : angle 0.02160 / 0.01 ( 2) hydrogen bonds : bond 0.03256 / 2.18 ( 286) hydrogen bonds : angle 4.02781 / 2.70 ( 825) Misc. bond : bond 0.00010 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.223 Fit side-chains REVERT: A 10 LYS cc_start: 0.7621 (mttt) cc_final: 0.6844 (tmtt) REVERT: A 239 MET cc_start: 0.7797 (tmm) cc_final: 0.7125 (mmm) REVERT: A 328 VAL cc_start: 0.9439 (m) cc_final: 0.9068 (t) REVERT: A 342 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7574 (tm-30) REVERT: B 78 LYS cc_start: 0.8356 (mtpt) cc_final: 0.8011 (mtmt) REVERT: B 153 ASP cc_start: 0.7841 (p0) cc_final: 0.7480 (p0) REVERT: B 262 MET cc_start: 0.8393 (tpt) cc_final: 0.7846 (tpp) REVERT: B 264 TYR cc_start: 0.8198 (m-80) cc_final: 0.7929 (m-80) REVERT: B 278 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7596 (m-10) REVERT: B 325 MET cc_start: 0.7987 (mmt) cc_final: 0.7653 (tpp) REVERT: G 20 ASP cc_start: 0.8217 (m-30) cc_final: 0.7401 (p0) REVERT: G 32 LEU cc_start: 0.8162 (pt) cc_final: 0.7896 (pp) REVERT: G 36 CYS cc_start: 0.7417 (OUTLIER) cc_final: 0.7067 (p) REVERT: R 44 MET cc_start: 0.8807 (tpp) cc_final: 0.8591 (tpp) REVERT: R 176 SER cc_start: 0.8944 (p) cc_final: 0.8611 (m) REVERT: R 183 MET cc_start: 0.8825 (mmt) cc_final: 0.8404 (mmp) REVERT: R 190 ASP cc_start: 0.7382 (p0) cc_final: 0.7011 (p0) REVERT: R 201 GLU cc_start: 0.7304 (tp30) cc_final: 0.6842 (tp30) REVERT: R 231 LYS cc_start: 0.8878 (ttmt) cc_final: 0.8637 (ttmm) REVERT: R 253 MET cc_start: 0.8738 (tpp) cc_final: 0.8501 (tpp) REVERT: R 286 ILE cc_start: 0.8564 (tt) cc_final: 0.8209 (mm) outliers start: 18 outliers final: 13 residues processed: 156 average time/residue: 0.0911 time to fit residues: 19.2607 Evaluate side-chains 146 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 292 TYR Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 297 THR Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 309 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 72 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.0270 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.120393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.095485 restraints weight = 15671.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.098530 restraints weight = 8688.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.100607 restraints weight = 5962.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.101996 restraints weight = 4630.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.102710 restraints weight = 3917.271| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7685 Z= 0.118 Angle : 0.675 11.895 10397 Z= 0.331 Chirality : 0.042 0.261 1157 Planarity : 0.004 0.074 1326 Dihedral : 4.551 34.049 1025 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.07 % Allowed : 29.88 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.29), residues: 938 helix: 1.55 (0.30), residues: 348 sheet: -1.06 (0.47), residues: 138 loop : -2.40 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 193 TYR 0.021 0.001 TYR B 111 PHE 0.020 0.001 PHE B 199 TRP 0.034 0.001 TRP B 82 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 7683) covalent geometry : angle 0.67543 / 0.33 (10395) SS BOND : bond 0.00042 / 0.02 ( 1) SS BOND : angle 0.09793 / 0.05 ( 2) hydrogen bonds : bond 0.03425 / 2.31 ( 286) hydrogen bonds : angle 3.98787 / 2.68 ( 825) Misc. bond : bond 0.00014 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1289.66 seconds wall clock time: 23 minutes 10.99 seconds (1390.99 seconds total)