Starting phenix.real_space_refine on Thu Jul 2 23:44:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7evz_31342/07_2026/7evz_31342.cif Found real_map, /net/cci-nas-00/data/ceres_data/7evz_31342/07_2026/7evz_31342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7evz_31342/07_2026/7evz_31342.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7evz_31342/07_2026/7evz_31342.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7evz_31342/07_2026/7evz_31342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7evz_31342/07_2026/7evz_31342.map" model { file = "/net/cci-nas-00/data/ceres_data/7evz_31342/07_2026/7evz_31342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7evz_31342/07_2026/7evz_31342.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.097 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1983 atoms to isotropic. 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 64 5.16 5 C 5810 2.51 5 N 1521 2.21 5 O 1683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9078 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1838 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "D" Number of atoms: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2296 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 6, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "D" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Unusual residues: {'JER': 1, 'PLM': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 2.11, per 1000 atoms: 0.23 Number of scatterers: 9078 At special positions: 0 Unit cell: (90.63, 123.975, 128.25, 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 64 16.00 O 1683 8.00 N 1521 7.00 C 5810 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 191 " distance=2.03 Simple disulfide: pdb=" SG CYS D 282 " - pdb=" SG CYS D 287 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 353.2 milliseconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 12 sheets defined 36.0% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 6 through 28 removed outlier: 3.521A pdb=" N LYS A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.582A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.591A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 216' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 271 through 279 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.750A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.939A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 351 removed outlier: 4.060A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.583A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.633A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 24 removed outlier: 4.224A pdb=" N GLN C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 23 through 33 Processing helix chain 'D' and resid 49 through 73 removed outlier: 3.576A pdb=" N THR D 73 " --> pdb=" O THR D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 105 removed outlier: 3.503A pdb=" N TYR D 82 " --> pdb=" O ARG D 78 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE D 83 " --> pdb=" O PRO D 79 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 84 " --> pdb=" O MET D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 110 removed outlier: 3.746A pdb=" N THR D 109 " --> pdb=" O GLY D 106 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR D 110 " --> pdb=" O ALA D 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 106 through 110' Processing helix chain 'D' and resid 113 through 148 removed outlier: 3.512A pdb=" N GLU D 121 " --> pdb=" O TRP D 117 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS D 148 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 181 removed outlier: 4.248A pdb=" N LEU D 160 " --> pdb=" O ASN D 156 " (cutoff:3.500A) Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 199 through 236 removed outlier: 3.510A pdb=" N ILE D 203 " --> pdb=" O HIS D 199 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL D 228 " --> pdb=" O ILE D 224 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG D 234 " --> pdb=" O THR D 230 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 235 " --> pdb=" O ARG D 231 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR D 236 " --> pdb=" O SER D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 268 removed outlier: 3.545A pdb=" N LYS D 256 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR D 257 " --> pdb=" O ALA D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 282 removed outlier: 3.977A pdb=" N VAL D 280 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY D 281 " --> pdb=" O LEU D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 314 removed outlier: 3.866A pdb=" N LEU D 297 " --> pdb=" O ALA D 293 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA D 300 " --> pdb=" O PHE D 296 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) Proline residue: D 308 - end of helix Processing helix chain 'D' and resid 315 through 325 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.545A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.555A pdb=" N PHE A 199 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 3.544A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.940A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 114 removed outlier: 3.502A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.959A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 190 through 192 removed outlier: 3.536A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.528A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.599A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.512A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.676A pdb=" N VAL E 12 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.506A pdb=" N VAL E 147 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1149 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.60 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2274 1.33 - 1.45: 1913 1.45 - 1.58: 4974 1.58 - 1.70: 3 1.70 - 1.82: 91 Bond restraints: 9255 Sorted by residual: bond pdb=" C31 JER D 401 " pdb=" C32 JER D 401 " ideal model delta sigma weight residual 1.543 1.361 0.182 2.00e-02 2.50e+03 8.29e+01 bond pdb=" C28 JER D 401 " pdb=" C29 JER D 401 " ideal model delta sigma weight residual 1.532 1.354 0.178 2.00e-02 2.50e+03 7.88e+01 bond pdb=" C28 JER D 401 " pdb=" C32 JER D 401 " ideal model delta sigma weight residual 1.537 1.651 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C10 JER D 401 " pdb=" C15 JER D 401 " ideal model delta sigma weight residual 1.460 1.374 0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C22 JER D 401 " pdb=" O23 JER D 401 " ideal model delta sigma weight residual 1.332 1.410 -0.078 2.00e-02 2.50e+03 1.53e+01 ... (remaining 9250 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 12372 2.34 - 4.68: 105 4.68 - 7.03: 18 7.03 - 9.37: 2 9.37 - 11.71: 3 Bond angle restraints: 12500 Sorted by residual: angle pdb=" N PHE D 237 " pdb=" CA PHE D 237 " pdb=" C PHE D 237 " ideal model delta sigma weight residual 111.36 123.07 -11.71 1.09e+00 8.42e-01 1.15e+02 angle pdb=" N ARG D 238 " pdb=" CA ARG D 238 " pdb=" C ARG D 238 " ideal model delta sigma weight residual 113.16 123.13 -9.97 1.24e+00 6.50e-01 6.46e+01 angle pdb=" N LYS D 239 " pdb=" CA LYS D 239 " pdb=" C LYS D 239 " ideal model delta sigma weight residual 110.23 116.35 -6.12 1.45e+00 4.76e-01 1.78e+01 angle pdb=" N THR D 236 " pdb=" CA THR D 236 " pdb=" C THR D 236 " ideal model delta sigma weight residual 109.54 103.76 5.78 1.37e+00 5.33e-01 1.78e+01 angle pdb=" C26 JER D 401 " pdb=" C28 JER D 401 " pdb=" C29 JER D 401 " ideal model delta sigma weight residual 114.08 102.52 11.56 3.00e+00 1.11e-01 1.48e+01 ... (remaining 12495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5006 17.98 - 35.95: 423 35.95 - 53.93: 65 53.93 - 71.91: 11 71.91 - 89.88: 6 Dihedral angle restraints: 5511 sinusoidal: 2191 harmonic: 3320 Sorted by residual: dihedral pdb=" CB CYS D 184 " pdb=" SG CYS D 184 " pdb=" SG CYS D 191 " pdb=" CB CYS D 191 " ideal model delta sinusoidal sigma weight residual -86.00 -47.75 -38.25 1 1.00e+01 1.00e-02 2.06e+01 dihedral pdb=" CB CYS E 159 " pdb=" SG CYS E 159 " pdb=" SG CYS E 229 " pdb=" CB CYS E 229 " ideal model delta sinusoidal sigma weight residual 93.00 65.20 27.80 1 1.00e+01 1.00e-02 1.11e+01 dihedral pdb=" CA ASP A 229 " pdb=" CB ASP A 229 " pdb=" CG ASP A 229 " pdb=" OD1 ASP A 229 " ideal model delta sinusoidal sigma weight residual -30.00 -87.29 57.29 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 5508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1357 0.093 - 0.186: 62 0.186 - 0.280: 4 0.280 - 0.373: 0 0.373 - 0.466: 1 Chirality restraints: 1424 Sorted by residual: chirality pdb=" CA PHE D 237 " pdb=" N PHE D 237 " pdb=" C PHE D 237 " pdb=" CB PHE D 237 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.43e+00 chirality pdb=" CA GLU D 249 " pdb=" N GLU D 249 " pdb=" C GLU D 249 " pdb=" CB GLU D 249 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA SER D 251 " pdb=" N SER D 251 " pdb=" C SER D 251 " pdb=" CB SER D 251 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 1421 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 235 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.54e+00 pdb=" N PRO E 236 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO E 236 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 236 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " 0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO C 49 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 239 " 0.007 2.00e-02 2.50e+03 1.50e-02 2.24e+00 pdb=" C LYS D 239 " -0.026 2.00e-02 2.50e+03 pdb=" O LYS D 239 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN D 240 " 0.009 2.00e-02 2.50e+03 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 289 2.71 - 3.26: 8624 3.26 - 3.80: 13751 3.80 - 4.35: 16884 4.35 - 4.90: 30032 Nonbonded interactions: 69580 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.160 3.040 nonbonded pdb=" OG SER D 192 " pdb=" O LEU D 195 " model vdw 2.180 3.040 nonbonded pdb=" OD2 ASP A 341 " pdb=" NZ LYS D 239 " model vdw 2.206 3.120 nonbonded pdb=" O THR D 236 " pdb=" OG1 THR D 236 " model vdw 2.218 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.259 3.040 ... (remaining 69575 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.660 Find NCS groups from input model: 0.060 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:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 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 : 0.004 0.182 9258 Z= 0.229 Angle : 0.585 11.711 12506 Z= 0.336 Chirality : 0.043 0.466 1424 Planarity : 0.003 0.053 1557 Dihedral : 13.304 89.882 3360 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.30 % Allowed : 5.18 % Favored : 94.52 % 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: -1.99 (0.23), residues: 1126 helix: 0.22 (0.24), residues: 382 sheet: -1.46 (0.29), residues: 277 loop : -2.53 (0.23), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 8 TYR 0.014 0.001 TYR E 190 PHE 0.020 0.001 PHE E 108 TRP 0.019 0.001 TRP E 176 HIS 0.003 0.000 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.23 ( 9255) covalent geometry : angle 0.58492 / 0.34 (12500) SS BOND : bond 0.00065 / 0.03 ( 3) SS BOND : angle 0.84701 / 0.45 ( 6) hydrogen bonds : bond 0.18619 / 12.54 ( 398) hydrogen bonds : angle 6.32723 / 4.34 ( 1149) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 152 time to evaluate : 0.360 Fit side-chains REVERT: B 44 GLN cc_start: 0.7722 (tp40) cc_final: 0.7430 (mt0) REVERT: B 137 ARG cc_start: 0.7464 (tpp-160) cc_final: 0.6979 (tpt90) REVERT: B 197 ARG cc_start: 0.7291 (tpp80) cc_final: 0.7004 (tpp80) REVERT: B 217 MET cc_start: 0.7100 (ptt) cc_final: 0.6529 (ptm) REVERT: B 274 THR cc_start: 0.8559 (m) cc_final: 0.8235 (p) REVERT: B 280 LYS cc_start: 0.8172 (tptp) cc_final: 0.7920 (tptt) REVERT: B 289 TYR cc_start: 0.8866 (m-80) cc_final: 0.7606 (m-80) REVERT: B 292 PHE cc_start: 0.8510 (m-10) cc_final: 0.8252 (m-10) REVERT: B 312 ASP cc_start: 0.8438 (t0) cc_final: 0.8035 (t0) REVERT: D 190 SER cc_start: 0.6529 (m) cc_final: 0.6206 (t) REVERT: D 224 ILE cc_start: 0.6056 (tt) cc_final: 0.5765 (tt) REVERT: D 292 ARG cc_start: 0.8190 (mtt90) cc_final: 0.7508 (mtm180) REVERT: E 93 MET cc_start: 0.6976 (ttm) cc_final: 0.6027 (ttm) REVERT: E 192 MET cc_start: 0.5588 (tpp) cc_final: 0.4274 (ptp) outliers start: 3 outliers final: 2 residues processed: 155 average time/residue: 0.1206 time to fit residues: 24.4037 Evaluate side-chains 121 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 119 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 249 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.1980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.0170 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 overall best weight: 0.5620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN B 6 GLN B 75 GLN B 110 ASN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 HIS D 240 ASN E 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.184101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.127071 restraints weight = 10229.226| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.39 r_work: 0.3343 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9258 Z= 0.101 Angle : 0.496 7.404 12506 Z= 0.255 Chirality : 0.039 0.148 1424 Planarity : 0.003 0.059 1557 Dihedral : 5.447 66.371 1308 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.12 % Allowed : 11.68 % Favored : 87.21 % 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: -0.82 (0.24), residues: 1126 helix: 1.69 (0.26), residues: 380 sheet: -1.11 (0.31), residues: 278 loop : -2.11 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 21 TYR 0.016 0.001 TYR E 190 PHE 0.015 0.001 PHE E 108 TRP 0.011 0.001 TRP E 176 HIS 0.003 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 9255) covalent geometry : angle 0.49554 / 0.26 (12500) SS BOND : bond 0.00243 / 0.12 ( 3) SS BOND : angle 0.57957 / 0.32 ( 6) hydrogen bonds : bond 0.03803 / 2.56 ( 398) hydrogen bonds : angle 4.36288 / 3.00 ( 1149) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.336 Fit side-chains REVERT: A 247 MET cc_start: 0.7842 (mtp) cc_final: 0.7591 (mtp) REVERT: B 118 ASP cc_start: 0.7997 (t0) cc_final: 0.7672 (t0) REVERT: B 197 ARG cc_start: 0.6782 (tpp80) cc_final: 0.6546 (tpp80) REVERT: B 217 MET cc_start: 0.6551 (ptt) cc_final: 0.6196 (ptm) REVERT: B 274 THR cc_start: 0.8320 (m) cc_final: 0.7873 (p) REVERT: B 280 LYS cc_start: 0.7586 (tptp) cc_final: 0.7376 (tptt) REVERT: B 292 PHE cc_start: 0.7949 (m-10) cc_final: 0.7618 (m-10) REVERT: B 312 ASP cc_start: 0.8432 (t0) cc_final: 0.7767 (t0) REVERT: D 224 ILE cc_start: 0.5766 (tt) cc_final: 0.5512 (tt) REVERT: E 82 GLN cc_start: 0.6778 (tp-100) cc_final: 0.6429 (tp40) REVERT: E 93 MET cc_start: 0.5707 (ttm) cc_final: 0.5147 (ttm) REVERT: E 140 MET cc_start: 0.8158 (mmm) cc_final: 0.7738 (mmm) REVERT: E 192 MET cc_start: 0.5626 (tpp) cc_final: 0.4000 (ptp) outliers start: 11 outliers final: 7 residues processed: 137 average time/residue: 0.1117 time to fit residues: 20.3764 Evaluate side-chains 128 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 34 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN D 303 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.177356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.120128 restraints weight = 10216.060| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 3.37 r_work: 0.3261 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9258 Z= 0.161 Angle : 0.544 7.787 12506 Z= 0.281 Chirality : 0.041 0.183 1424 Planarity : 0.004 0.065 1557 Dihedral : 5.716 70.862 1304 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.23 % Allowed : 14.11 % Favored : 83.65 % 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: -0.45 (0.25), residues: 1126 helix: 2.13 (0.26), residues: 381 sheet: -1.00 (0.31), residues: 278 loop : -1.97 (0.25), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 21 TYR 0.020 0.002 TYR E 190 PHE 0.018 0.001 PHE A 189 TRP 0.013 0.001 TRP E 176 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 ( 9255) covalent geometry : angle 0.54366 / 0.28 (12500) SS BOND : bond 0.00279 / 0.14 ( 3) SS BOND : angle 0.77603 / 0.43 ( 6) hydrogen bonds : bond 0.04182 / 2.82 ( 398) hydrogen bonds : angle 4.15243 / 2.88 ( 1149) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 247 MET cc_start: 0.7837 (mtp) cc_final: 0.7578 (mtp) REVERT: A 275 GLU cc_start: 0.7959 (tp30) cc_final: 0.7650 (mm-30) REVERT: B 175 GLN cc_start: 0.7095 (pt0) cc_final: 0.6068 (pm20) REVERT: B 217 MET cc_start: 0.6550 (ptt) cc_final: 0.6231 (ptm) REVERT: B 280 LYS cc_start: 0.7652 (tptp) cc_final: 0.7445 (tptt) REVERT: B 292 PHE cc_start: 0.8123 (m-10) cc_final: 0.7874 (m-10) REVERT: B 312 ASP cc_start: 0.8386 (t0) cc_final: 0.7697 (t0) REVERT: D 151 LEU cc_start: 0.6444 (OUTLIER) cc_final: 0.6224 (tt) REVERT: D 180 MET cc_start: 0.6901 (mmt) cc_final: 0.6665 (mpp) REVERT: D 190 SER cc_start: 0.5671 (m) cc_final: 0.5320 (t) REVERT: E 82 GLN cc_start: 0.6771 (tp-100) cc_final: 0.6406 (tp40) REVERT: E 140 MET cc_start: 0.8144 (mmm) cc_final: 0.7660 (mmm) outliers start: 22 outliers final: 15 residues processed: 150 average time/residue: 0.1027 time to fit residues: 20.7386 Evaluate side-chains 143 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 68 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 16 optimal weight: 0.0770 chunk 91 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS B 6 GLN B 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.178044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.119854 restraints weight = 10452.975| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 3.47 r_work: 0.3246 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9258 Z= 0.150 Angle : 0.530 8.091 12506 Z= 0.274 Chirality : 0.041 0.177 1424 Planarity : 0.004 0.064 1557 Dihedral : 5.738 69.849 1304 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.05 % Allowed : 16.45 % Favored : 80.51 % 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: -0.28 (0.25), residues: 1126 helix: 2.31 (0.27), residues: 381 sheet: -0.95 (0.31), residues: 277 loop : -1.88 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 21 TYR 0.023 0.001 TYR E 235 PHE 0.014 0.001 PHE A 189 TRP 0.011 0.001 TRP E 47 HIS 0.003 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 9255) covalent geometry : angle 0.52826 / 0.27 (12500) SS BOND : bond 0.00513 / 0.26 ( 3) SS BOND : angle 1.84950 / 1.05 ( 6) hydrogen bonds : bond 0.03924 / 2.66 ( 398) hydrogen bonds : angle 3.99915 / 2.77 ( 1149) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.298 Fit side-chains REVERT: A 247 MET cc_start: 0.7812 (mtp) cc_final: 0.7548 (mtp) REVERT: A 297 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7879 (tp30) REVERT: A 306 GLN cc_start: 0.7279 (tp40) cc_final: 0.6984 (tp40) REVERT: B 175 GLN cc_start: 0.7120 (pt0) cc_final: 0.6078 (pm20) REVERT: B 217 MET cc_start: 0.6587 (ptt) cc_final: 0.6279 (ptm) REVERT: B 292 PHE cc_start: 0.8078 (m-10) cc_final: 0.7843 (m-10) REVERT: B 312 ASP cc_start: 0.8411 (t0) cc_final: 0.7692 (t0) REVERT: D 151 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.6221 (tt) REVERT: D 180 MET cc_start: 0.6971 (mmt) cc_final: 0.6713 (mpp) REVERT: D 190 SER cc_start: 0.6349 (m) cc_final: 0.5865 (t) REVERT: E 82 GLN cc_start: 0.6690 (tp-100) cc_final: 0.6281 (tp40) REVERT: E 93 MET cc_start: 0.5973 (ttp) cc_final: 0.5207 (ttm) REVERT: E 140 MET cc_start: 0.8124 (mmm) cc_final: 0.7625 (mmm) outliers start: 30 outliers final: 21 residues processed: 152 average time/residue: 0.1028 time to fit residues: 21.0758 Evaluate side-chains 146 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 5 optimal weight: 0.0170 chunk 46 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 87 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 25 optimal weight: 0.0270 chunk 80 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN ** D 63 ASN ** 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 = 0.4055 r_free = 0.4055 target = 0.178881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.122359 restraints weight = 10250.794| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 3.43 r_work: 0.3290 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9258 Z= 0.094 Angle : 0.485 7.219 12506 Z= 0.247 Chirality : 0.039 0.159 1424 Planarity : 0.003 0.062 1557 Dihedral : 5.770 66.647 1304 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.83 % Allowed : 18.58 % Favored : 79.59 % 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: -0.07 (0.25), residues: 1126 helix: 2.53 (0.27), residues: 380 sheet: -0.82 (0.31), residues: 277 loop : -1.79 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 21 TYR 0.020 0.001 TYR E 235 PHE 0.013 0.001 PHE E 108 TRP 0.008 0.001 TRP B 211 HIS 0.002 0.000 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 ( 9255) covalent geometry : angle 0.48448 / 0.25 (12500) SS BOND : bond 0.00190 / 0.09 ( 3) SS BOND : angle 1.02580 / 0.58 ( 6) hydrogen bonds : bond 0.03217 / 2.18 ( 398) hydrogen bonds : angle 3.73004 / 2.58 ( 1149) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.333 Fit side-chains REVERT: A 247 MET cc_start: 0.7914 (mtp) cc_final: 0.7649 (mtp) REVERT: A 306 GLN cc_start: 0.7323 (tp40) cc_final: 0.7061 (tp40) REVERT: B 217 MET cc_start: 0.6773 (ptt) cc_final: 0.6434 (ptm) REVERT: B 292 PHE cc_start: 0.8050 (m-10) cc_final: 0.7767 (m-10) REVERT: B 304 ARG cc_start: 0.8231 (ttp80) cc_final: 0.7958 (ttp-170) REVERT: B 312 ASP cc_start: 0.8477 (t0) cc_final: 0.7743 (t0) REVERT: D 180 MET cc_start: 0.6909 (mmt) cc_final: 0.6671 (mpp) REVERT: D 190 SER cc_start: 0.6442 (m) cc_final: 0.6000 (t) REVERT: E 82 GLN cc_start: 0.6707 (tp-100) cc_final: 0.6266 (tp40) REVERT: E 192 MET cc_start: 0.6588 (tpp) cc_final: 0.4158 (ptp) outliers start: 18 outliers final: 15 residues processed: 146 average time/residue: 0.0996 time to fit residues: 19.6981 Evaluate side-chains 143 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 71 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 60 optimal weight: 0.0870 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN A 346 ASN B 32 GLN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.174385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.117821 restraints weight = 10291.847| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 3.41 r_work: 0.3231 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9258 Z= 0.153 Angle : 0.535 7.600 12506 Z= 0.275 Chirality : 0.041 0.181 1424 Planarity : 0.004 0.064 1557 Dihedral : 6.033 69.470 1304 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.74 % Allowed : 18.98 % Favored : 78.27 % 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: -0.06 (0.26), residues: 1126 helix: 2.48 (0.27), residues: 381 sheet: -0.77 (0.32), residues: 275 loop : -1.77 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 197 TYR 0.024 0.001 TYR E 235 PHE 0.014 0.001 PHE E 108 TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 ( 9255) covalent geometry : angle 0.53464 / 0.27 (12500) SS BOND : bond 0.00262 / 0.13 ( 3) SS BOND : angle 1.00093 / 0.57 ( 6) hydrogen bonds : bond 0.03830 / 2.60 ( 398) hydrogen bonds : angle 3.87515 / 2.69 ( 1149) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.403 Fit side-chains REVERT: A 247 MET cc_start: 0.7920 (mtp) cc_final: 0.7629 (mtp) REVERT: A 306 GLN cc_start: 0.7335 (tp40) cc_final: 0.7077 (tp40) REVERT: B 19 ARG cc_start: 0.7434 (ttp-170) cc_final: 0.7208 (ttp-170) REVERT: B 175 GLN cc_start: 0.7442 (pt0) cc_final: 0.6383 (pm20) REVERT: B 217 MET cc_start: 0.6764 (ptt) cc_final: 0.6437 (ptm) REVERT: B 292 PHE cc_start: 0.8149 (m-10) cc_final: 0.7898 (m-10) REVERT: B 312 ASP cc_start: 0.8444 (t0) cc_final: 0.7704 (t0) REVERT: D 151 LEU cc_start: 0.6544 (OUTLIER) cc_final: 0.6321 (tt) REVERT: D 180 MET cc_start: 0.7237 (mmt) cc_final: 0.7032 (mpp) REVERT: D 190 SER cc_start: 0.6498 (m) cc_final: 0.6035 (t) REVERT: E 82 GLN cc_start: 0.6794 (tp-100) cc_final: 0.6355 (tp40) REVERT: E 192 MET cc_start: 0.6478 (OUTLIER) cc_final: 0.4168 (ptp) outliers start: 27 outliers final: 21 residues processed: 140 average time/residue: 0.1024 time to fit residues: 19.6689 Evaluate side-chains 146 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 81 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN ** D 63 ASN ** 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 = 0.3956 r_free = 0.3956 target = 0.170362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.111663 restraints weight = 10114.596| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.42 r_work: 0.3197 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 9258 Z= 0.108 Angle : 0.502 8.107 12506 Z= 0.255 Chirality : 0.040 0.163 1424 Planarity : 0.003 0.063 1557 Dihedral : 5.884 70.648 1304 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.64 % Allowed : 20.00 % Favored : 77.36 % 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: 0.03 (0.26), residues: 1126 helix: 2.59 (0.27), residues: 380 sheet: -0.71 (0.32), residues: 275 loop : -1.74 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 197 TYR 0.023 0.001 TYR E 235 PHE 0.016 0.001 PHE E 108 TRP 0.008 0.001 TRP B 211 HIS 0.003 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 9255) covalent geometry : angle 0.50151 / 0.26 (12500) SS BOND : bond 0.00209 / 0.10 ( 3) SS BOND : angle 0.78471 / 0.46 ( 6) hydrogen bonds : bond 0.03384 / 2.29 ( 398) hydrogen bonds : angle 3.73340 / 2.59 ( 1149) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.325 Fit side-chains REVERT: A 247 MET cc_start: 0.8086 (mtp) cc_final: 0.7801 (mtp) REVERT: A 297 GLU cc_start: 0.8318 (tp30) cc_final: 0.8117 (tp30) REVERT: A 306 GLN cc_start: 0.7427 (tp40) cc_final: 0.7141 (tp40) REVERT: B 19 ARG cc_start: 0.7520 (ttp-170) cc_final: 0.7291 (ttp-170) REVERT: B 118 ASP cc_start: 0.8238 (t0) cc_final: 0.7935 (t0) REVERT: B 172 GLU cc_start: 0.8705 (tt0) cc_final: 0.8443 (tt0) REVERT: B 175 GLN cc_start: 0.7664 (pt0) cc_final: 0.6614 (pm20) REVERT: B 217 MET cc_start: 0.7111 (ptt) cc_final: 0.6742 (ptm) REVERT: B 292 PHE cc_start: 0.8256 (m-10) cc_final: 0.8014 (m-10) REVERT: B 312 ASP cc_start: 0.8545 (t0) cc_final: 0.7878 (t0) REVERT: D 151 LEU cc_start: 0.6692 (OUTLIER) cc_final: 0.6476 (tt) REVERT: D 180 MET cc_start: 0.7323 (mmt) cc_final: 0.7110 (mpp) REVERT: D 190 SER cc_start: 0.6479 (m) cc_final: 0.6069 (t) REVERT: E 82 GLN cc_start: 0.6888 (tp-100) cc_final: 0.6423 (tp40) REVERT: E 93 MET cc_start: 0.6324 (ttp) cc_final: 0.5757 (ttm) REVERT: E 192 MET cc_start: 0.6457 (OUTLIER) cc_final: 0.4272 (ptp) outliers start: 26 outliers final: 19 residues processed: 147 average time/residue: 0.0973 time to fit residues: 19.5200 Evaluate side-chains 148 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 19 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 90 optimal weight: 0.0020 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN ** D 63 ASN ** 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 = 0.3959 r_free = 0.3959 target = 0.171091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.112711 restraints weight = 10085.768| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.44 r_work: 0.3198 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 9258 Z= 0.104 Angle : 0.497 8.587 12506 Z= 0.253 Chirality : 0.039 0.162 1424 Planarity : 0.004 0.063 1557 Dihedral : 5.659 68.245 1304 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.94 % Allowed : 20.30 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.26), residues: 1126 helix: 2.66 (0.27), residues: 380 sheet: -0.62 (0.32), residues: 275 loop : -1.67 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 21 TYR 0.022 0.001 TYR E 235 PHE 0.016 0.001 PHE E 108 TRP 0.008 0.001 TRP E 47 HIS 0.003 0.000 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 ( 9255) covalent geometry : angle 0.49660 / 0.25 (12500) SS BOND : bond 0.00220 / 0.11 ( 3) SS BOND : angle 0.82076 / 0.45 ( 6) hydrogen bonds : bond 0.03264 / 2.21 ( 398) hydrogen bonds : angle 3.66869 / 2.55 ( 1149) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.339 Fit side-chains REVERT: A 32 ARG cc_start: 0.8168 (ptp-110) cc_final: 0.7795 (mtm110) REVERT: A 247 MET cc_start: 0.7997 (mtp) cc_final: 0.7718 (mtp) REVERT: A 306 GLN cc_start: 0.7309 (tp40) cc_final: 0.7015 (tp40) REVERT: B 19 ARG cc_start: 0.7482 (ttp-170) cc_final: 0.7263 (ttp-170) REVERT: B 118 ASP cc_start: 0.8202 (t0) cc_final: 0.7872 (t0) REVERT: B 172 GLU cc_start: 0.8693 (tt0) cc_final: 0.8436 (tt0) REVERT: B 175 GLN cc_start: 0.7585 (pt0) cc_final: 0.6479 (pm20) REVERT: B 217 MET cc_start: 0.6970 (ptt) cc_final: 0.6607 (ptm) REVERT: B 234 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7485 (t80) REVERT: B 292 PHE cc_start: 0.8169 (m-10) cc_final: 0.7862 (m-10) REVERT: B 312 ASP cc_start: 0.8534 (t0) cc_final: 0.7801 (t0) REVERT: C 42 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7004 (mm-30) REVERT: D 151 LEU cc_start: 0.6510 (OUTLIER) cc_final: 0.6286 (tt) REVERT: D 180 MET cc_start: 0.7260 (mmt) cc_final: 0.7047 (mpp) REVERT: D 190 SER cc_start: 0.6409 (m) cc_final: 0.6033 (t) REVERT: D 282 CYS cc_start: 0.6924 (OUTLIER) cc_final: 0.6622 (t) REVERT: E 82 GLN cc_start: 0.6885 (tp-100) cc_final: 0.6434 (tp40) REVERT: E 93 MET cc_start: 0.6177 (ttp) cc_final: 0.5614 (ttm) REVERT: E 192 MET cc_start: 0.6362 (OUTLIER) cc_final: 0.4193 (ptp) outliers start: 29 outliers final: 22 residues processed: 148 average time/residue: 0.0890 time to fit residues: 18.3193 Evaluate side-chains 157 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 1.9990 chunk 91 optimal weight: 0.1980 chunk 94 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN ** D 63 ASN ** 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 = 0.3956 r_free = 0.3956 target = 0.170647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.112448 restraints weight = 10002.151| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.43 r_work: 0.3193 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9258 Z= 0.115 Angle : 0.514 9.346 12506 Z= 0.261 Chirality : 0.040 0.164 1424 Planarity : 0.004 0.063 1557 Dihedral : 5.621 67.871 1304 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.94 % Allowed : 20.20 % Favored : 76.85 % 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: 0.14 (0.26), residues: 1126 helix: 2.65 (0.27), residues: 381 sheet: -0.60 (0.32), residues: 275 loop : -1.71 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 21 TYR 0.023 0.001 TYR E 235 PHE 0.016 0.001 PHE E 108 TRP 0.008 0.001 TRP E 47 HIS 0.002 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 ( 9255) covalent geometry : angle 0.51342 / 0.26 (12500) SS BOND : bond 0.00216 / 0.11 ( 3) SS BOND : angle 0.94934 / 0.50 ( 6) hydrogen bonds : bond 0.03353 / 2.27 ( 398) hydrogen bonds : angle 3.68280 / 2.56 ( 1149) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.309 Fit side-chains REVERT: A 32 ARG cc_start: 0.8125 (ptp-110) cc_final: 0.7754 (mtm110) REVERT: A 247 MET cc_start: 0.7992 (mtp) cc_final: 0.7703 (mtp) REVERT: A 306 GLN cc_start: 0.7345 (tp40) cc_final: 0.7076 (tp40) REVERT: B 19 ARG cc_start: 0.7502 (ttp-170) cc_final: 0.7287 (ttp-170) REVERT: B 118 ASP cc_start: 0.8214 (t0) cc_final: 0.7886 (t0) REVERT: B 172 GLU cc_start: 0.8702 (tt0) cc_final: 0.8428 (tt0) REVERT: B 175 GLN cc_start: 0.7589 (pt0) cc_final: 0.6491 (pm20) REVERT: B 217 MET cc_start: 0.6974 (ptt) cc_final: 0.6619 (ptm) REVERT: B 234 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7462 (t80) REVERT: B 292 PHE cc_start: 0.8168 (m-10) cc_final: 0.7859 (m-10) REVERT: B 312 ASP cc_start: 0.8495 (t0) cc_final: 0.7759 (t0) REVERT: C 42 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7017 (mm-30) REVERT: D 151 LEU cc_start: 0.6515 (OUTLIER) cc_final: 0.6290 (tt) REVERT: D 180 MET cc_start: 0.7261 (mmt) cc_final: 0.7050 (mpp) REVERT: D 190 SER cc_start: 0.6404 (m) cc_final: 0.6058 (t) REVERT: D 282 CYS cc_start: 0.6889 (OUTLIER) cc_final: 0.6624 (t) REVERT: E 82 GLN cc_start: 0.6897 (tp-100) cc_final: 0.6438 (tp40) REVERT: E 93 MET cc_start: 0.6205 (ttp) cc_final: 0.5603 (ttm) REVERT: E 192 MET cc_start: 0.6396 (OUTLIER) cc_final: 0.4219 (ptp) outliers start: 29 outliers final: 21 residues processed: 146 average time/residue: 0.0863 time to fit residues: 17.3764 Evaluate side-chains 151 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 99 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 104 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN ** D 63 ASN ** 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 = 0.4016 r_free = 0.4016 target = 0.176134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.116781 restraints weight = 10119.644| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.56 r_work: 0.3201 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 9258 Z= 0.108 Angle : 0.510 9.215 12506 Z= 0.259 Chirality : 0.039 0.159 1424 Planarity : 0.004 0.063 1557 Dihedral : 5.484 67.073 1304 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.74 % Allowed : 20.20 % Favored : 77.06 % 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: 0.17 (0.26), residues: 1126 helix: 2.71 (0.27), residues: 380 sheet: -0.60 (0.32), residues: 278 loop : -1.70 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 21 TYR 0.022 0.001 TYR E 235 PHE 0.016 0.001 PHE E 108 TRP 0.008 0.001 TRP E 47 HIS 0.002 0.000 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 9255) covalent geometry : angle 0.51009 / 0.26 (12500) SS BOND : bond 0.00207 / 0.10 ( 3) SS BOND : angle 0.90516 / 0.48 ( 6) hydrogen bonds : bond 0.03265 / 2.21 ( 398) hydrogen bonds : angle 3.65460 / 2.54 ( 1149) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.207 Fit side-chains REVERT: A 32 ARG cc_start: 0.8117 (ptp-110) cc_final: 0.7726 (mtm110) REVERT: A 306 GLN cc_start: 0.7387 (tp40) cc_final: 0.7112 (tp40) REVERT: B 19 ARG cc_start: 0.7524 (ttp-170) cc_final: 0.7306 (ttp-170) REVERT: B 118 ASP cc_start: 0.8240 (t0) cc_final: 0.7918 (t0) REVERT: B 172 GLU cc_start: 0.8707 (tt0) cc_final: 0.8436 (tt0) REVERT: B 175 GLN cc_start: 0.7623 (pt0) cc_final: 0.6523 (pm20) REVERT: B 217 MET cc_start: 0.7029 (ptt) cc_final: 0.6637 (ptm) REVERT: B 234 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7456 (t80) REVERT: B 292 PHE cc_start: 0.8145 (m-10) cc_final: 0.7838 (m-10) REVERT: B 312 ASP cc_start: 0.8497 (t0) cc_final: 0.7794 (t0) REVERT: C 42 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7027 (mm-30) REVERT: D 151 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.6319 (tt) REVERT: D 180 MET cc_start: 0.7282 (mmt) cc_final: 0.7069 (mpp) REVERT: D 190 SER cc_start: 0.6418 (m) cc_final: 0.6088 (t) REVERT: D 282 CYS cc_start: 0.6874 (OUTLIER) cc_final: 0.6615 (t) REVERT: E 82 GLN cc_start: 0.6889 (tp-100) cc_final: 0.6428 (tp40) REVERT: E 93 MET cc_start: 0.6233 (ttp) cc_final: 0.5650 (ttm) REVERT: E 192 MET cc_start: 0.6353 (OUTLIER) cc_final: 0.4221 (ptp) outliers start: 27 outliers final: 23 residues processed: 143 average time/residue: 0.0867 time to fit residues: 16.8702 Evaluate side-chains 155 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 10 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 80 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN ** D 63 ASN ** 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 = 0.3967 r_free = 0.3967 target = 0.171848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.113695 restraints weight = 9953.518| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 3.42 r_work: 0.3210 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 9258 Z= 0.102 Angle : 0.504 9.071 12506 Z= 0.255 Chirality : 0.039 0.156 1424 Planarity : 0.004 0.063 1557 Dihedral : 5.254 64.653 1304 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.64 % Allowed : 20.51 % Favored : 76.85 % 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: 0.19 (0.26), residues: 1126 helix: 2.74 (0.27), residues: 380 sheet: -0.60 (0.32), residues: 278 loop : -1.69 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 21 TYR 0.022 0.001 TYR E 235 PHE 0.016 0.001 PHE E 108 TRP 0.007 0.001 TRP E 47 HIS 0.002 0.000 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 ( 9255) covalent geometry : angle 0.50339 / 0.26 (12500) SS BOND : bond 0.00219 / 0.11 ( 3) SS BOND : angle 0.85745 / 0.45 ( 6) hydrogen bonds : bond 0.03147 / 2.13 ( 398) hydrogen bonds : angle 3.61313 / 2.51 ( 1149) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2395.18 seconds wall clock time: 41 minutes 50.72 seconds (2510.72 seconds total)