Starting phenix.real_space_refine on Thu Jul 2 16:05:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8f7w_28911/07_2026/8f7w_28911.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f7w_28911/07_2026/8f7w_28911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f7w_28911/07_2026/8f7w_28911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f7w_28911/07_2026/8f7w_28911.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8f7w_28911/07_2026/8f7w_28911.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8f7w_28911/07_2026/8f7w_28911.cif" model { file = "/net/cci-nas-00/data/ceres_data/8f7w_28911/07_2026/8f7w_28911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f7w_28911/07_2026/8f7w_28911.cif" } resolution = 3.19 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= -0.000 sd= 0.008 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 66 5.16 5 C 5822 2.51 5 N 1511 2.21 5 O 1688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s 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: 9087 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2277 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain: "P" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 69 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "A" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1826 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 224} Chain breaks: 1 Chain: "B" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2576 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 329} Chain: "C" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 427 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "E" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1792 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Chain: "R" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 120 Unusual residues: {'CLR': 3, 'PLM': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 1.93, per 1000 atoms: 0.21 Number of scatterers: 9087 At special positions: 0 Unit cell: (104.958, 112.455, 133.875, 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 66 16.00 O 1688 8.00 N 1511 7.00 C 5822 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 210 " 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: 0.49 Conformation dependent library (CDL) restraints added in 381.7 milliseconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 15 sheets defined 38.2% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'R' and resid 57 through 86 Processing helix chain 'R' and resid 92 through 110 removed outlier: 3.787A pdb=" N ILE R 96 " --> pdb=" O THR R 92 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR R 110 " --> pdb=" O ALA R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 122 Processing helix chain 'R' and resid 127 through 162 Processing helix chain 'R' and resid 162 through 168 removed outlier: 3.657A pdb=" N LEU R 167 " --> pdb=" O PRO R 163 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP R 168 " --> pdb=" O VAL R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 196 removed outlier: 3.635A pdb=" N SER R 188 " --> pdb=" O LEU R 184 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL R 189 " --> pdb=" O LEU R 185 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 217 No H-bonds generated for 'chain 'R' and resid 215 through 217' Processing helix chain 'R' and resid 218 through 255 removed outlier: 4.689A pdb=" N ILE R 237 " --> pdb=" O PHE R 233 " (cutoff:3.500A) Proline residue: R 238 - end of helix removed outlier: 3.738A pdb=" N SER R 255 " --> pdb=" O LEU R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 300 Proline residue: R 289 - end of helix Processing helix chain 'R' and resid 305 through 331 removed outlier: 3.775A pdb=" N SER R 323 " --> pdb=" O GLY R 319 " (cutoff:3.500A) Proline residue: R 327 - end of helix Processing helix chain 'R' and resid 334 through 342 removed outlier: 3.765A pdb=" N ARG R 339 " --> pdb=" O GLU R 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.963A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 55 Processing helix chain 'A' and resid 208 through 213 removed outlier: 4.296A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.501A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.083A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.761A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.822A pdb=" N TYR C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.892A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.850A pdb=" N SER E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.118A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 225 removed outlier: 3.714A pdb=" N VAL E 225 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 197 through 202 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.949A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.329A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.833A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.377A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.145A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.133A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.372A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.787A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.612A pdb=" N SER E 71 " --> pdb=" O PHE E 80 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AB3, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.603A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 141 through 143 removed outlier: 3.711A pdb=" N PHE E 213 " --> pdb=" O CYS E 160 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 147 through 149 removed outlier: 3.538A pdb=" N GLU E 247 " --> pdb=" O VAL E 148 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 190 through 191 445 hydrogen bonds defined for protein. 1278 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: 1.62 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2865 1.34 - 1.46: 1935 1.46 - 1.58: 4378 1.58 - 1.69: 1 1.69 - 1.81: 96 Bond restraints: 9275 Sorted by residual: bond pdb=" C ILE R 237 " pdb=" N PRO R 238 " ideal model delta sigma weight residual 1.335 1.363 -0.028 1.36e-02 5.41e+03 4.09e+00 bond pdb=" C ILE R 58 " pdb=" N PRO R 59 " ideal model delta sigma weight residual 1.336 1.359 -0.024 1.23e-02 6.61e+03 3.75e+00 bond pdb=" CA THR R 288 " pdb=" C THR R 288 " ideal model delta sigma weight residual 1.522 1.546 -0.024 1.26e-02 6.30e+03 3.56e+00 bond pdb=" CA VAL R 207 " pdb=" CB VAL R 207 " ideal model delta sigma weight residual 1.546 1.578 -0.032 1.75e-02 3.27e+03 3.44e+00 bond pdb=" C THR R 288 " pdb=" N PRO R 289 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.41e+00 ... (remaining 9270 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 12083 1.83 - 3.66: 395 3.66 - 5.49: 66 5.49 - 7.32: 20 7.32 - 9.15: 3 Bond angle restraints: 12567 Sorted by residual: angle pdb=" CA ARG E 219 " pdb=" CB ARG E 219 " pdb=" CG ARG E 219 " ideal model delta sigma weight residual 114.10 122.80 -8.70 2.00e+00 2.50e-01 1.89e+01 angle pdb=" C ARG E 192 " pdb=" N MET E 193 " pdb=" CA MET E 193 " ideal model delta sigma weight residual 125.02 131.16 -6.14 1.76e+00 3.23e-01 1.22e+01 angle pdb=" CA ARG A 32 " pdb=" CB ARG A 32 " pdb=" CG ARG A 32 " ideal model delta sigma weight residual 114.10 120.37 -6.27 2.00e+00 2.50e-01 9.83e+00 angle pdb=" C MET R 121 " pdb=" N ASN R 122 " pdb=" CA ASN R 122 " ideal model delta sigma weight residual 124.31 129.53 -5.22 1.67e+00 3.59e-01 9.78e+00 angle pdb=" C TYR R 139 " pdb=" N TYR R 140 " pdb=" CA TYR R 140 " ideal model delta sigma weight residual 120.79 124.99 -4.20 1.39e+00 5.18e-01 9.13e+00 ... (remaining 12562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.18: 5273 14.18 - 28.36: 176 28.36 - 42.53: 37 42.53 - 56.71: 3 56.71 - 70.89: 1 Dihedral angle restraints: 5490 sinusoidal: 2166 harmonic: 3324 Sorted by residual: dihedral pdb=" C ILE R 58 " pdb=" N ILE R 58 " pdb=" CA ILE R 58 " pdb=" CB ILE R 58 " ideal model delta harmonic sigma weight residual -122.00 -131.61 9.61 0 2.50e+00 1.60e-01 1.48e+01 dihedral pdb=" CA HIS B 266 " pdb=" C HIS B 266 " pdb=" N ASP B 267 " pdb=" CA ASP B 267 " ideal model delta harmonic sigma weight residual -180.00 -160.95 -19.05 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 161.89 18.11 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 5487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1290 0.089 - 0.177: 138 0.177 - 0.266: 7 0.266 - 0.355: 3 0.355 - 0.443: 4 Chirality restraints: 1442 Sorted by residual: chirality pdb=" CB ILE R 58 " pdb=" CA ILE R 58 " pdb=" CG1 ILE R 58 " pdb=" CG2 ILE R 58 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.91e+00 chirality pdb=" C14 CLR R 403 " pdb=" C13 CLR R 403 " pdb=" C15 CLR R 403 " pdb=" C8 CLR R 403 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.43 2.00e-01 2.50e+01 4.56e+00 chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 1439 not shown) Planarity restraints: 1563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER R 220 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.19e+00 pdb=" C SER R 220 " 0.046 2.00e-02 2.50e+03 pdb=" O SER R 220 " -0.017 2.00e-02 2.50e+03 pdb=" N TRP R 221 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 232 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C ILE R 232 " -0.038 2.00e-02 2.50e+03 pdb=" O ILE R 232 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE R 233 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS E 35 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.74e+00 pdb=" C HIS E 35 " 0.038 2.00e-02 2.50e+03 pdb=" O HIS E 35 " -0.014 2.00e-02 2.50e+03 pdb=" N TRP E 36 " -0.013 2.00e-02 2.50e+03 ... (remaining 1560 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2226 2.81 - 3.33: 7797 3.33 - 3.85: 14396 3.85 - 4.38: 16496 4.38 - 4.90: 29335 Nonbonded interactions: 70250 Sorted by model distance: nonbonded pdb=" O ALA R 317 " pdb=" OG1 THR R 321 " model vdw 2.282 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.318 3.040 nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.326 3.040 nonbonded pdb=" O ILE B 123 " pdb=" OG SER B 136 " model vdw 2.358 3.040 nonbonded pdb=" O ILE E 139 " pdb=" OG1 THR E 239 " model vdw 2.361 3.040 ... (remaining 70245 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.690 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 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 0.060 9276 Z= 0.209 Angle : 0.801 9.154 12569 Z= 0.443 Chirality : 0.059 0.443 1442 Planarity : 0.006 0.051 1563 Dihedral : 8.056 70.889 3343 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.10 % Allowed : 0.91 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.21), residues: 1129 helix: -0.66 (0.22), residues: 399 sheet: -0.83 (0.29), residues: 287 loop : -1.80 (0.24), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 68 TYR 0.025 0.002 TYR E 50 PHE 0.024 0.002 PHE A 189 TRP 0.021 0.002 TRP E 111 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.21 ( 9275) covalent geometry : angle 0.80006 / 0.44 (12567) SS BOND : bond 0.00558 / 0.29 ( 1) SS BOND : angle 2.33652 / 1.56 ( 2) hydrogen bonds : bond 0.12925 / 8.77 ( 445) hydrogen bonds : angle 6.39993 / 4.56 ( 1278) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 239 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 180 ILE cc_start: 0.6785 (OUTLIER) cc_final: 0.6569 (mp) REVERT: R 297 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7402 (mt-10) REVERT: A 337 ASP cc_start: 0.7854 (m-30) cc_final: 0.7607 (m-30) REVERT: B 211 TRP cc_start: 0.8414 (m100) cc_final: 0.8062 (m100) REVERT: C 41 CYS cc_start: 0.7950 (m) cc_final: 0.7489 (m) outliers start: 1 outliers final: 0 residues processed: 240 average time/residue: 0.1103 time to fit residues: 35.3568 Evaluate side-chains 171 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 170 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 180 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 141 ASN R 322 ASN B 75 GLN B 266 HIS E 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.182228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.144422 restraints weight = 10417.555| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.14 r_work: 0.3394 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9276 Z= 0.147 Angle : 0.531 6.888 12569 Z= 0.281 Chirality : 0.042 0.237 1442 Planarity : 0.004 0.032 1563 Dihedral : 4.385 37.262 1299 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.03 % Allowed : 6.69 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.24), residues: 1129 helix: 1.13 (0.25), residues: 405 sheet: -0.57 (0.29), residues: 292 loop : -1.10 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 257 TYR 0.017 0.002 TYR R 140 PHE 0.014 0.001 PHE A 189 TRP 0.015 0.002 TRP E 111 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 9275) covalent geometry : angle 0.52965 / 0.28 (12567) SS BOND : bond 0.01575 / 0.83 ( 1) SS BOND : angle 2.81155 / 1.87 ( 2) hydrogen bonds : bond 0.03991 / 2.62 ( 445) hydrogen bonds : angle 4.78059 / 3.39 ( 1278) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: R 297 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7273 (mt-10) REVERT: P 211 PHE cc_start: 0.8732 (m-80) cc_final: 0.8425 (m-80) REVERT: A 33 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7746 (mt-10) REVERT: A 232 LEU cc_start: 0.8178 (mt) cc_final: 0.7848 (mp) REVERT: B 46 ARG cc_start: 0.8047 (mtt180) cc_final: 0.7832 (mtp85) REVERT: B 98 SER cc_start: 0.8929 (m) cc_final: 0.8728 (t) REVERT: B 153 ASP cc_start: 0.8019 (m-30) cc_final: 0.7642 (m-30) REVERT: B 247 ASP cc_start: 0.7480 (t0) cc_final: 0.7177 (t0) REVERT: C 38 MET cc_start: 0.7084 (mtp) cc_final: 0.6879 (mtp) REVERT: E 93 MET cc_start: 0.8557 (ttm) cc_final: 0.8340 (ttt) REVERT: E 161 ARG cc_start: 0.7103 (tpp-160) cc_final: 0.6804 (tpp-160) REVERT: E 236 TYR cc_start: 0.8435 (m-80) cc_final: 0.8213 (m-80) outliers start: 20 outliers final: 15 residues processed: 185 average time/residue: 0.1072 time to fit residues: 26.9836 Evaluate side-chains 169 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 218 ASP Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 266 ASP Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 239 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 48 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 ASN E 232 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.177108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.137973 restraints weight = 10253.861| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.14 r_work: 0.3344 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9276 Z= 0.135 Angle : 0.512 6.325 12569 Z= 0.267 Chirality : 0.041 0.215 1442 Planarity : 0.003 0.040 1563 Dihedral : 4.210 28.519 1297 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.93 % Allowed : 9.32 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.25), residues: 1129 helix: 1.81 (0.26), residues: 407 sheet: -0.49 (0.29), residues: 298 loop : -0.80 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 24 TYR 0.014 0.001 TYR R 140 PHE 0.017 0.002 PHE R 126 TRP 0.014 0.001 TRP B 99 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 9275) covalent geometry : angle 0.51133 / 0.27 (12567) SS BOND : bond 0.00141 / 0.07 ( 1) SS BOND : angle 2.38601 / 1.59 ( 2) hydrogen bonds : bond 0.03774 / 2.48 ( 445) hydrogen bonds : angle 4.55350 / 3.24 ( 1278) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: R 297 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7252 (mt-10) REVERT: A 33 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7607 (mt-10) REVERT: A 232 LEU cc_start: 0.8177 (mt) cc_final: 0.7841 (mp) REVERT: A 318 GLU cc_start: 0.6824 (mm-30) cc_final: 0.6505 (mm-30) REVERT: B 46 ARG cc_start: 0.8230 (mtt180) cc_final: 0.7940 (mtp85) REVERT: B 153 ASP cc_start: 0.8163 (m-30) cc_final: 0.7827 (m-30) REVERT: B 247 ASP cc_start: 0.7763 (t0) cc_final: 0.7462 (t0) REVERT: E 82 GLN cc_start: 0.8086 (mm110) cc_final: 0.7879 (mm110) REVERT: E 161 ARG cc_start: 0.7192 (tpp-160) cc_final: 0.6978 (tpp-160) outliers start: 19 outliers final: 12 residues processed: 169 average time/residue: 0.1058 time to fit residues: 24.5357 Evaluate side-chains 162 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 218 ASP Chi-restraints excluded: chain R residue 266 ASP Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 220 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 72 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 269 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 = 0.4174 r_free = 0.4174 target = 0.183659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.138709 restraints weight = 10561.530| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.55 r_work: 0.3302 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9276 Z= 0.141 Angle : 0.512 7.330 12569 Z= 0.265 Chirality : 0.041 0.203 1442 Planarity : 0.003 0.033 1563 Dihedral : 4.234 29.226 1297 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.33 % Allowed : 10.13 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.25), residues: 1129 helix: 2.08 (0.26), residues: 408 sheet: -0.31 (0.28), residues: 302 loop : -0.70 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 314 TYR 0.014 0.001 TYR R 140 PHE 0.012 0.001 PHE B 235 TRP 0.012 0.001 TRP E 111 HIS 0.005 0.001 HIS E 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 9275) covalent geometry : angle 0.51122 / 0.26 (12567) SS BOND : bond 0.00303 / 0.16 ( 1) SS BOND : angle 2.24157 / 1.49 ( 2) hydrogen bonds : bond 0.03721 / 2.43 ( 445) hydrogen bonds : angle 4.50938 / 3.22 ( 1278) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7732 (mt-10) REVERT: A 232 LEU cc_start: 0.7852 (mt) cc_final: 0.7437 (mp) REVERT: A 329 THR cc_start: 0.7410 (OUTLIER) cc_final: 0.7079 (p) REVERT: B 46 ARG cc_start: 0.8384 (mtt180) cc_final: 0.7842 (mtp85) REVERT: B 153 ASP cc_start: 0.8004 (m-30) cc_final: 0.7726 (m-30) REVERT: B 247 ASP cc_start: 0.7784 (t0) cc_final: 0.7457 (t0) REVERT: C 41 CYS cc_start: 0.8205 (m) cc_final: 0.7979 (m) REVERT: E 161 ARG cc_start: 0.7334 (tpp-160) cc_final: 0.7005 (tpp-160) outliers start: 23 outliers final: 18 residues processed: 177 average time/residue: 0.1031 time to fit residues: 25.0554 Evaluate side-chains 167 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 218 ASP Chi-restraints excluded: chain R residue 243 ILE Chi-restraints excluded: chain R residue 266 ASP Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 239 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 100 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 268 ASN E 82 GLN E 195 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.179341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.134318 restraints weight = 10538.322| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.45 r_work: 0.3285 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9276 Z= 0.194 Angle : 0.558 7.942 12569 Z= 0.289 Chirality : 0.043 0.209 1442 Planarity : 0.003 0.032 1563 Dihedral : 4.682 29.387 1297 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.75 % Allowed : 10.13 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.25), residues: 1129 helix: 2.08 (0.25), residues: 403 sheet: -0.47 (0.28), residues: 303 loop : -0.60 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 314 TYR 0.013 0.002 TYR R 140 PHE 0.014 0.002 PHE R 143 TRP 0.015 0.002 TRP R 221 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.19 ( 9275) covalent geometry : angle 0.55653 / 0.29 (12567) SS BOND : bond 0.00347 / 0.18 ( 1) SS BOND : angle 2.78131 / 1.85 ( 2) hydrogen bonds : bond 0.04214 / 2.75 ( 445) hydrogen bonds : angle 4.58232 / 3.27 ( 1278) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 159 time to evaluate : 0.342 Fit side-chains REVERT: R 297 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7288 (mt-10) REVERT: A 232 LEU cc_start: 0.7847 (mt) cc_final: 0.7432 (mp) REVERT: A 329 THR cc_start: 0.7467 (OUTLIER) cc_final: 0.7116 (p) REVERT: B 46 ARG cc_start: 0.8436 (mtt180) cc_final: 0.7849 (mtp85) REVERT: B 153 ASP cc_start: 0.8154 (m-30) cc_final: 0.7840 (m-30) REVERT: B 247 ASP cc_start: 0.7951 (t0) cc_final: 0.7697 (t0) REVERT: B 334 SER cc_start: 0.8631 (m) cc_final: 0.8316 (t) REVERT: E 82 GLN cc_start: 0.8323 (mm110) cc_final: 0.8090 (mm110) REVERT: E 198 SER cc_start: 0.8987 (m) cc_final: 0.8746 (p) outliers start: 37 outliers final: 28 residues processed: 185 average time/residue: 0.1083 time to fit residues: 27.2865 Evaluate side-chains 178 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 218 ASP Chi-restraints excluded: chain R residue 243 ILE Chi-restraints excluded: chain R residue 266 ASP Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 218 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 86 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.181051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.141302 restraints weight = 10542.513| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.36 r_work: 0.3231 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9276 Z= 0.152 Angle : 0.534 8.747 12569 Z= 0.274 Chirality : 0.042 0.202 1442 Planarity : 0.003 0.031 1563 Dihedral : 4.592 29.026 1297 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.24 % Allowed : 10.94 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.25), residues: 1129 helix: 2.13 (0.25), residues: 405 sheet: -0.37 (0.29), residues: 302 loop : -0.55 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 314 TYR 0.013 0.001 TYR R 140 PHE 0.012 0.001 PHE R 143 TRP 0.012 0.001 TRP B 99 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 9275) covalent geometry : angle 0.53321 / 0.27 (12567) SS BOND : bond 0.00380 / 0.20 ( 1) SS BOND : angle 2.50909 / 1.67 ( 2) hydrogen bonds : bond 0.03900 / 2.55 ( 445) hydrogen bonds : angle 4.49249 / 3.21 ( 1278) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.361 Fit side-chains REVERT: R 297 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7267 (mt-10) REVERT: A 232 LEU cc_start: 0.7733 (mt) cc_final: 0.7272 (mp) REVERT: A 329 THR cc_start: 0.7437 (OUTLIER) cc_final: 0.7104 (p) REVERT: B 46 ARG cc_start: 0.8432 (mtt180) cc_final: 0.7798 (mtp85) REVERT: B 153 ASP cc_start: 0.8171 (m-30) cc_final: 0.7766 (m-30) REVERT: B 215 GLU cc_start: 0.7282 (tm-30) cc_final: 0.7015 (tm-30) REVERT: B 247 ASP cc_start: 0.7964 (t0) cc_final: 0.7662 (t0) REVERT: B 334 SER cc_start: 0.8656 (m) cc_final: 0.8352 (t) REVERT: E 158 ILE cc_start: 0.7145 (OUTLIER) cc_final: 0.6779 (pt) REVERT: E 198 SER cc_start: 0.9007 (m) cc_final: 0.8727 (p) outliers start: 32 outliers final: 29 residues processed: 176 average time/residue: 0.1102 time to fit residues: 26.3226 Evaluate side-chains 173 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 171 THR Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 218 ASP Chi-restraints excluded: chain R residue 243 ILE Chi-restraints excluded: chain R residue 266 ASP Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 218 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 44 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 82 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.183490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.143467 restraints weight = 10663.939| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.39 r_work: 0.3182 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9276 Z= 0.172 Angle : 0.543 9.279 12569 Z= 0.281 Chirality : 0.042 0.203 1442 Planarity : 0.003 0.031 1563 Dihedral : 4.669 30.994 1297 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.85 % Allowed : 11.45 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.25), residues: 1129 helix: 2.13 (0.25), residues: 404 sheet: -0.38 (0.29), residues: 307 loop : -0.50 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 134 TYR 0.012 0.001 TYR R 140 PHE 0.012 0.002 PHE E 27 TRP 0.012 0.002 TRP B 99 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 ( 9275) covalent geometry : angle 0.54230 / 0.28 (12567) SS BOND : bond 0.00363 / 0.19 ( 1) SS BOND : angle 2.61587 / 1.74 ( 2) hydrogen bonds : bond 0.03979 / 2.60 ( 445) hydrogen bonds : angle 4.52212 / 3.23 ( 1278) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 0.353 Fit side-chains REVERT: R 297 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7087 (mt-10) REVERT: A 232 LEU cc_start: 0.7661 (mt) cc_final: 0.7196 (mp) REVERT: A 315 ASP cc_start: 0.7648 (OUTLIER) cc_final: 0.7425 (m-30) REVERT: A 329 THR cc_start: 0.7361 (OUTLIER) cc_final: 0.7055 (p) REVERT: B 46 ARG cc_start: 0.8408 (mtt180) cc_final: 0.7725 (mtp85) REVERT: B 153 ASP cc_start: 0.8208 (m-30) cc_final: 0.7803 (m-30) REVERT: B 217 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7096 (ptm) REVERT: B 247 ASP cc_start: 0.7943 (t0) cc_final: 0.7659 (t0) REVERT: B 334 SER cc_start: 0.8616 (m) cc_final: 0.8300 (t) REVERT: E 82 GLN cc_start: 0.8329 (mm110) cc_final: 0.8114 (mm110) REVERT: E 158 ILE cc_start: 0.7110 (OUTLIER) cc_final: 0.6755 (pt) REVERT: E 198 SER cc_start: 0.9000 (m) cc_final: 0.8698 (p) outliers start: 38 outliers final: 27 residues processed: 170 average time/residue: 0.1095 time to fit residues: 25.2628 Evaluate side-chains 183 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 171 THR Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 218 ASP Chi-restraints excluded: chain R residue 243 ILE Chi-restraints excluded: chain R residue 266 ASP Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 218 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 5 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 89 optimal weight: 0.0970 chunk 81 optimal weight: 0.0980 chunk 69 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.183550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.144633 restraints weight = 10563.594| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.34 r_work: 0.3376 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9276 Z= 0.099 Angle : 0.492 9.499 12569 Z= 0.253 Chirality : 0.041 0.207 1442 Planarity : 0.003 0.031 1563 Dihedral : 4.291 31.698 1297 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.43 % Allowed : 12.97 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.26), residues: 1129 helix: 2.41 (0.26), residues: 406 sheet: -0.16 (0.29), residues: 302 loop : -0.37 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 134 TYR 0.012 0.001 TYR R 140 PHE 0.010 0.001 PHE E 240 TRP 0.009 0.001 TRP B 63 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 9275) covalent geometry : angle 0.49116 / 0.25 (12567) SS BOND : bond 0.00444 / 0.23 ( 1) SS BOND : angle 1.99857 / 1.33 ( 2) hydrogen bonds : bond 0.03349 / 2.18 ( 445) hydrogen bonds : angle 4.32424 / 3.09 ( 1278) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.338 Fit side-chains REVERT: R 297 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7317 (mt-10) REVERT: A 33 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7522 (mt-10) REVERT: A 298 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8118 (tt0) REVERT: A 315 ASP cc_start: 0.7672 (OUTLIER) cc_final: 0.7461 (m-30) REVERT: A 329 THR cc_start: 0.7334 (OUTLIER) cc_final: 0.7003 (p) REVERT: B 46 ARG cc_start: 0.8442 (mtt180) cc_final: 0.7873 (mtp85) REVERT: B 153 ASP cc_start: 0.8072 (m-30) cc_final: 0.7710 (m-30) REVERT: B 247 ASP cc_start: 0.7992 (t0) cc_final: 0.7705 (t0) REVERT: B 334 SER cc_start: 0.8627 (m) cc_final: 0.8397 (t) REVERT: E 22 CYS cc_start: 0.8219 (t) cc_final: 0.7968 (t) REVERT: E 46 GLU cc_start: 0.8006 (tt0) cc_final: 0.7517 (mt-10) REVERT: E 82 GLN cc_start: 0.8236 (mm110) cc_final: 0.7988 (mm110) REVERT: E 158 ILE cc_start: 0.7100 (OUTLIER) cc_final: 0.6825 (pt) REVERT: E 161 ARG cc_start: 0.7335 (tpp-160) cc_final: 0.7091 (tpp-160) outliers start: 24 outliers final: 18 residues processed: 168 average time/residue: 0.1009 time to fit residues: 23.3410 Evaluate side-chains 166 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 66 TYR Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 218 ASP Chi-restraints excluded: chain R residue 243 ILE Chi-restraints excluded: chain R residue 266 ASP Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 214 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 100 ASN R 122 ASN R 179 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.177088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.132727 restraints weight = 10562.455| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.47 r_work: 0.3385 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 9276 Z= 0.246 Angle : 0.617 10.110 12569 Z= 0.316 Chirality : 0.045 0.200 1442 Planarity : 0.003 0.032 1563 Dihedral : 5.017 36.551 1297 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.84 % Allowed : 13.17 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.25), residues: 1129 helix: 2.01 (0.25), residues: 404 sheet: -0.52 (0.29), residues: 302 loop : -0.45 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 134 TYR 0.016 0.002 TYR E 94 PHE 0.017 0.002 PHE E 27 TRP 0.014 0.002 TRP R 221 HIS 0.005 0.002 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.25 ( 9275) covalent geometry : angle 0.61578 / 0.32 (12567) SS BOND : bond 0.00290 / 0.15 ( 1) SS BOND : angle 3.02802 / 2.02 ( 2) hydrogen bonds : bond 0.04536 / 2.97 ( 445) hydrogen bonds : angle 4.64676 / 3.32 ( 1278) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: R 297 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7215 (mt-10) REVERT: A 329 THR cc_start: 0.7348 (OUTLIER) cc_final: 0.7031 (p) REVERT: B 19 ARG cc_start: 0.6655 (ttp-170) cc_final: 0.5711 (mtm180) REVERT: B 46 ARG cc_start: 0.8505 (mtt180) cc_final: 0.7932 (mtp85) REVERT: B 153 ASP cc_start: 0.8439 (m-30) cc_final: 0.8066 (m-30) REVERT: B 247 ASP cc_start: 0.8053 (t0) cc_final: 0.7790 (t0) REVERT: B 262 MET cc_start: 0.8247 (mtp) cc_final: 0.7993 (mtp) REVERT: B 334 SER cc_start: 0.8727 (m) cc_final: 0.8358 (t) REVERT: E 82 GLN cc_start: 0.8233 (mm110) cc_final: 0.7984 (mm110) REVERT: E 158 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.7108 (pt) REVERT: E 231 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7640 (tpp) outliers start: 28 outliers final: 22 residues processed: 160 average time/residue: 0.1147 time to fit residues: 24.7578 Evaluate side-chains 162 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 171 THR Chi-restraints excluded: chain R residue 218 ASP Chi-restraints excluded: chain R residue 243 ILE Chi-restraints excluded: chain R residue 266 ASP Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 231 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 100 optimal weight: 0.0040 chunk 23 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 15 optimal weight: 0.0870 chunk 41 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.5972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 100 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.185463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.145855 restraints weight = 10618.025| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.27 r_work: 0.3468 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9276 Z= 0.103 Angle : 0.511 10.582 12569 Z= 0.263 Chirality : 0.041 0.208 1442 Planarity : 0.003 0.030 1563 Dihedral : 4.491 33.452 1297 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.13 % Allowed : 13.98 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.26), residues: 1129 helix: 2.26 (0.26), residues: 409 sheet: -0.25 (0.29), residues: 299 loop : -0.31 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.013 0.001 TYR R 97 PHE 0.010 0.001 PHE A 189 TRP 0.010 0.001 TRP B 297 HIS 0.002 0.000 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 9275) covalent geometry : angle 0.51004 / 0.26 (12567) SS BOND : bond 0.00403 / 0.21 ( 1) SS BOND : angle 2.08382 / 1.39 ( 2) hydrogen bonds : bond 0.03453 / 2.24 ( 445) hydrogen bonds : angle 4.33625 / 3.11 ( 1278) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: R 297 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7213 (mt-10) REVERT: A 33 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7551 (mt-10) REVERT: A 287 TYR cc_start: 0.6446 (OUTLIER) cc_final: 0.5850 (p90) REVERT: A 329 THR cc_start: 0.7283 (OUTLIER) cc_final: 0.6937 (p) REVERT: B 19 ARG cc_start: 0.6786 (ttp-170) cc_final: 0.5972 (mtm180) REVERT: B 46 ARG cc_start: 0.8478 (mtt180) cc_final: 0.7940 (mtp85) REVERT: B 153 ASP cc_start: 0.8044 (m-30) cc_final: 0.7720 (m-30) REVERT: B 247 ASP cc_start: 0.8041 (t0) cc_final: 0.7781 (t0) REVERT: B 325 MET cc_start: 0.7991 (ttm) cc_final: 0.7764 (ttm) REVERT: B 334 SER cc_start: 0.8604 (m) cc_final: 0.8362 (t) REVERT: E 22 CYS cc_start: 0.8113 (t) cc_final: 0.7813 (t) REVERT: E 161 ARG cc_start: 0.7307 (tpp-160) cc_final: 0.7017 (tpp-160) outliers start: 21 outliers final: 17 residues processed: 167 average time/residue: 0.1080 time to fit residues: 24.4726 Evaluate side-chains 168 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 218 ASP Chi-restraints excluded: chain R residue 243 ILE Chi-restraints excluded: chain R residue 266 ASP Chi-restraints excluded: chain R residue 301 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 214 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 70 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 0.3980 chunk 42 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 122 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.184603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.145257 restraints weight = 10509.103| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.28 r_work: 0.3270 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9276 Z= 0.123 Angle : 0.517 10.718 12569 Z= 0.266 Chirality : 0.042 0.208 1442 Planarity : 0.003 0.030 1563 Dihedral : 4.413 31.625 1297 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.33 % Allowed : 14.08 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.25), residues: 1129 helix: 2.30 (0.25), residues: 406 sheet: -0.19 (0.29), residues: 304 loop : -0.27 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.012 0.001 TYR R 140 PHE 0.010 0.001 PHE A 189 TRP 0.011 0.001 TRP B 99 HIS 0.002 0.001 HIS R 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 9275) covalent geometry : angle 0.51666 / 0.27 (12567) SS BOND : bond 0.00414 / 0.22 ( 1) SS BOND : angle 2.20613 / 1.47 ( 2) hydrogen bonds : bond 0.03563 / 2.31 ( 445) hydrogen bonds : angle 4.31715 / 3.10 ( 1278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2879.27 seconds wall clock time: 50 minutes 12.17 seconds (3012.17 seconds total)