Starting phenix.real_space_refine on Sat Aug 23 02:38:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f7w_28911/08_2025/8f7w_28911.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f7w_28911/08_2025/8f7w_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_28911/08_2025/8f7w_28911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f7w_28911/08_2025/8f7w_28911.map" model { file = "/net/cci-nas-00/data/ceres_data/8f7w_28911/08_2025/8f7w_28911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f7w_28911/08_2025/8f7w_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 1.69, per 1000 atoms: 0.19 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: 0.62 Conformation dependent library (CDL) restraints added in 239.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.20 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: 1.12 Time building geometry restraints manager: 0.80 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: 5423 14.18 - 28.36: 186 28.36 - 42.53: 39 42.53 - 56.71: 9 56.71 - 70.89: 1 Dihedral angle restraints: 5658 sinusoidal: 2334 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 5655 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.820 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 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 : 8.286 70.889 3511 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 aren 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 covalent geometry : bond 0.00383 ( 9275) covalent geometry : angle 0.80006 (12567) SS BOND : bond 0.00558 ( 1) SS BOND : angle 2.33652 ( 2) hydrogen bonds : bond 0.12925 ( 445) hydrogen bonds : angle 6.39993 ( 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 : 0.285 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: 0.0977 time to fit residues: 31.2023 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 : 0.255 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4019 r_free = 0.4019 target = 0.180138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.142364 restraints weight = 10417.497| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.16 r_work: 0.3371 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9276 Z= 0.146 Angle : 0.535 6.876 12569 Z= 0.282 Chirality : 0.043 0.214 1442 Planarity : 0.004 0.032 1563 Dihedral : 5.421 44.081 1467 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.23 % Allowed : 6.48 % 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 aren not related in a simple way. whole: -0.25 (0.24), residues: 1129 helix: 1.17 (0.25), residues: 405 sheet: -0.58 (0.29), residues: 293 loop : -1.08 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 134 TYR 0.017 0.002 TYR R 140 PHE 0.014 0.002 PHE A 189 TRP 0.016 0.002 TRP B 99 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9275) covalent geometry : angle 0.53385 (12567) SS BOND : bond 0.03175 ( 1) SS BOND : angle 2.44496 ( 2) hydrogen bonds : bond 0.03937 ( 445) hydrogen bonds : angle 4.76777 ( 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 200 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: R 297 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7277 (mt-10) REVERT: P 211 PHE cc_start: 0.8667 (m-80) cc_final: 0.8380 (m-80) REVERT: A 33 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7521 (mt-10) REVERT: A 232 LEU cc_start: 0.8217 (mt) cc_final: 0.7924 (mp) REVERT: B 153 ASP cc_start: 0.7832 (m-30) cc_final: 0.7479 (m-30) REVERT: B 247 ASP cc_start: 0.7259 (t0) cc_final: 0.6987 (t0) REVERT: C 38 MET cc_start: 0.7042 (mtp) cc_final: 0.6832 (mtp) REVERT: E 93 MET cc_start: 0.8369 (ttm) cc_final: 0.8122 (ttt) REVERT: E 161 ARG cc_start: 0.7058 (tpp-160) cc_final: 0.6801 (tpp-160) outliers start: 22 outliers final: 16 residues processed: 189 average time/residue: 0.0863 time to fit residues: 22.1568 Evaluate side-chains 171 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 36 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 89 optimal weight: 0.4980 chunk 28 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 103 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4040 r_free = 0.4040 target = 0.182169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.144229 restraints weight = 10207.674| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.10 r_work: 0.3408 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9276 Z= 0.099 Angle : 0.477 6.530 12569 Z= 0.249 Chirality : 0.040 0.208 1442 Planarity : 0.003 0.039 1563 Dihedral : 4.970 44.276 1465 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.72 % Allowed : 9.42 % Favored : 88.86 % 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 aren not related in a simple way. whole: 0.40 (0.25), residues: 1129 helix: 1.92 (0.26), residues: 407 sheet: -0.37 (0.29), residues: 293 loop : -0.83 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 24 TYR 0.013 0.001 TYR R 140 PHE 0.015 0.001 PHE R 126 TRP 0.008 0.001 TRP B 99 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 9275) covalent geometry : angle 0.47622 (12567) SS BOND : bond 0.00110 ( 1) SS BOND : angle 1.99396 ( 2) hydrogen bonds : bond 0.03390 ( 445) hydrogen bonds : angle 4.48533 ( 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 182 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: R 297 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7339 (mt-10) REVERT: A 33 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7525 (mt-10) REVERT: A 232 LEU cc_start: 0.8156 (mt) cc_final: 0.7828 (mp) REVERT: A 298 GLU cc_start: 0.8016 (tt0) cc_final: 0.7721 (tt0) REVERT: B 153 ASP cc_start: 0.7965 (m-30) cc_final: 0.7603 (m-30) REVERT: B 247 ASP cc_start: 0.7564 (t0) cc_final: 0.7260 (t0) REVERT: C 41 CYS cc_start: 0.8090 (m) cc_final: 0.7874 (m) REVERT: E 161 ARG cc_start: 0.7133 (tpp-160) cc_final: 0.6878 (tpp-160) outliers start: 17 outliers final: 12 residues processed: 172 average time/residue: 0.0884 time to fit residues: 20.6676 Evaluate side-chains 168 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.225 ------------------------------------------------------------------------------- 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 290 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain E residue 155 SER 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: 3.9990 chunk 81 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.181953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.141574 restraints weight = 10586.087| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.32 r_work: 0.3238 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9276 Z= 0.188 Angle : 0.560 8.271 12569 Z= 0.290 Chirality : 0.043 0.208 1442 Planarity : 0.003 0.033 1563 Dihedral : 5.254 40.884 1465 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.13 % Allowed : 10.44 % Favored : 87.44 % 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 aren not related in a simple way. whole: 0.48 (0.25), residues: 1129 helix: 2.09 (0.26), residues: 399 sheet: -0.50 (0.28), residues: 299 loop : -0.69 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 314 TYR 0.016 0.002 TYR A 296 PHE 0.013 0.002 PHE A 189 TRP 0.014 0.002 TRP B 99 HIS 0.005 0.001 HIS E 233 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 9275) covalent geometry : angle 0.55871 (12567) SS BOND : bond 0.00397 ( 1) SS BOND : angle 2.46783 ( 2) hydrogen bonds : bond 0.04162 ( 445) hydrogen bonds : angle 4.62580 ( 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 184 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: R 297 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7177 (mt-10) REVERT: A 232 LEU cc_start: 0.7909 (mt) cc_final: 0.7512 (mp) REVERT: A 255 ASN cc_start: 0.7635 (m-40) cc_final: 0.7407 (m-40) REVERT: A 329 THR cc_start: 0.7406 (OUTLIER) cc_final: 0.7053 (p) REVERT: B 153 ASP cc_start: 0.8136 (m-30) cc_final: 0.7792 (m-30) REVERT: B 247 ASP cc_start: 0.7640 (t0) cc_final: 0.7328 (t0) REVERT: B 334 SER cc_start: 0.8681 (m) cc_final: 0.8355 (t) REVERT: E 161 ARG cc_start: 0.7357 (tpp-160) cc_final: 0.7027 (tpp-160) outliers start: 21 outliers final: 18 residues processed: 177 average time/residue: 0.0838 time to fit residues: 20.1019 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 : 0.252 ------------------------------------------------------------------------------- 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 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 65 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 189 SER 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 218 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 100 ASN A 255 ASN A 269 ASN B 259 GLN E 82 GLN E 195 ASN E 232 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.183670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.144091 restraints weight = 10465.327| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.39 r_work: 0.3244 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9276 Z= 0.123 Angle : 0.495 7.583 12569 Z= 0.256 Chirality : 0.041 0.223 1442 Planarity : 0.003 0.033 1563 Dihedral : 5.023 39.860 1465 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.94 % Allowed : 11.55 % Favored : 85.51 % 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 aren not related in a simple way. whole: 0.71 (0.25), residues: 1129 helix: 2.19 (0.26), residues: 406 sheet: -0.32 (0.28), residues: 302 loop : -0.56 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.013 0.001 TYR A 296 PHE 0.011 0.001 PHE A 189 TRP 0.009 0.001 TRP R 221 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9275) covalent geometry : angle 0.49401 (12567) SS BOND : bond 0.00363 ( 1) SS BOND : angle 2.20687 ( 2) hydrogen bonds : bond 0.03608 ( 445) hydrogen bonds : angle 4.41682 ( 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 181 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 0.205 Fit side-chains REVERT: R 62 ILE cc_start: 0.6235 (mm) cc_final: 0.6016 (tt) REVERT: A 232 LEU cc_start: 0.7752 (mt) cc_final: 0.7287 (mp) REVERT: A 255 ASN cc_start: 0.7361 (m110) cc_final: 0.7110 (m-40) REVERT: A 329 THR cc_start: 0.7367 (OUTLIER) cc_final: 0.7065 (p) REVERT: B 153 ASP cc_start: 0.8018 (m-30) cc_final: 0.7750 (m-30) REVERT: B 247 ASP cc_start: 0.7801 (t0) cc_final: 0.7495 (t0) REVERT: B 262 MET cc_start: 0.8327 (mtp) cc_final: 0.8095 (mtp) REVERT: C 15 LEU cc_start: 0.7620 (mt) cc_final: 0.7412 (mp) REVERT: C 41 CYS cc_start: 0.8387 (m) cc_final: 0.8127 (m) REVERT: E 161 ARG cc_start: 0.7307 (tpp-160) cc_final: 0.6975 (tpp-160) outliers start: 29 outliers final: 23 residues processed: 170 average time/residue: 0.0887 time to fit residues: 20.6431 Evaluate side-chains 165 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 120 LEU 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 269 ASN Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 324 THR 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 213 VAL 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 155 SER Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 239 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 86 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 89 optimal weight: 0.2980 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4147 r_free = 0.4147 target = 0.181132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.140331 restraints weight = 10539.907| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.33 r_work: 0.3226 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9276 Z= 0.135 Angle : 0.503 8.496 12569 Z= 0.261 Chirality : 0.041 0.220 1442 Planarity : 0.003 0.032 1563 Dihedral : 5.027 38.835 1465 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.24 % Allowed : 11.75 % Favored : 85.01 % 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 aren not related in a simple way. whole: 0.81 (0.25), residues: 1129 helix: 2.34 (0.25), residues: 404 sheet: -0.32 (0.28), residues: 302 loop : -0.53 (0.30), residues: 423 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 0.011 0.001 PHE A 189 TRP 0.010 0.001 TRP B 99 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9275) covalent geometry : angle 0.50248 (12567) SS BOND : bond 0.00373 ( 1) SS BOND : angle 2.25980 ( 2) hydrogen bonds : bond 0.03631 ( 445) hydrogen bonds : angle 4.39204 ( 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 175 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.358 Fit side-chains REVERT: A 193 ASP cc_start: 0.8588 (m-30) cc_final: 0.8376 (m-30) REVERT: A 232 LEU cc_start: 0.7747 (mt) cc_final: 0.7298 (mp) REVERT: A 318 GLU cc_start: 0.6632 (mm-30) cc_final: 0.6269 (mm-30) REVERT: A 329 THR cc_start: 0.7390 (OUTLIER) cc_final: 0.7078 (p) REVERT: B 153 ASP cc_start: 0.8102 (m-30) cc_final: 0.7806 (m-30) REVERT: B 247 ASP cc_start: 0.7774 (t0) cc_final: 0.7434 (t0) REVERT: E 161 ARG cc_start: 0.7333 (tpp-160) cc_final: 0.6986 (tpp-160) REVERT: E 198 SER cc_start: 0.8956 (m) cc_final: 0.8729 (p) outliers start: 32 outliers final: 28 residues processed: 163 average time/residue: 0.0916 time to fit residues: 20.3627 Evaluate side-chains 169 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 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 172 GLU Chi-restraints excluded: chain B residue 213 VAL 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 156 VAL Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 239 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 44 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 100 ASN A 269 ASN E 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.180596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.139936 restraints weight = 10578.394| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.31 r_work: 0.3212 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3966 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= 0.165 Angle : 0.530 8.429 12569 Z= 0.274 Chirality : 0.042 0.220 1442 Planarity : 0.003 0.031 1563 Dihedral : 5.217 36.867 1465 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.44 % Allowed : 11.65 % Favored : 84.90 % 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 aren not related in a simple way. whole: 0.81 (0.25), residues: 1129 helix: 2.31 (0.25), residues: 404 sheet: -0.35 (0.28), residues: 302 loop : -0.47 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 134 TYR 0.011 0.001 TYR R 140 PHE 0.018 0.001 PHE R 143 TRP 0.013 0.002 TRP R 221 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 9275) covalent geometry : angle 0.52912 (12567) SS BOND : bond 0.00359 ( 1) SS BOND : angle 2.52605 ( 2) hydrogen bonds : bond 0.03890 ( 445) hydrogen bonds : angle 4.42992 ( 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 188 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.318 Fit side-chains REVERT: R 297 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7078 (mt-10) REVERT: A 232 LEU cc_start: 0.7659 (mt) cc_final: 0.7206 (mp) REVERT: A 329 THR cc_start: 0.7441 (OUTLIER) cc_final: 0.7099 (p) REVERT: B 153 ASP cc_start: 0.8137 (m-30) cc_final: 0.7761 (m-30) REVERT: B 247 ASP cc_start: 0.7901 (t0) cc_final: 0.7625 (t0) REVERT: B 334 SER cc_start: 0.8624 (m) cc_final: 0.8292 (t) REVERT: E 198 SER cc_start: 0.8958 (m) cc_final: 0.8719 (p) outliers start: 34 outliers final: 27 residues processed: 176 average time/residue: 0.0914 time to fit residues: 21.8276 Evaluate side-chains 176 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 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 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 218 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 5 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 68 optimal weight: 6.9990 chunk 89 optimal weight: 0.3980 chunk 81 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 122 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN E 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.180368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.139678 restraints weight = 10636.458| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.44 r_work: 0.3226 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9276 Z= 0.108 Angle : 0.504 9.219 12569 Z= 0.258 Chirality : 0.041 0.227 1442 Planarity : 0.003 0.031 1563 Dihedral : 5.003 36.288 1465 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.84 % Allowed : 12.36 % Favored : 84.80 % 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 aren not related in a simple way. whole: 0.98 (0.25), residues: 1129 helix: 2.44 (0.26), residues: 406 sheet: -0.24 (0.28), residues: 302 loop : -0.38 (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 0.013 0.001 PHE A 267 TRP 0.010 0.001 TRP R 221 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 9275) covalent geometry : angle 0.50332 (12567) SS BOND : bond 0.00413 ( 1) SS BOND : angle 2.07270 ( 2) hydrogen bonds : bond 0.03459 ( 445) hydrogen bonds : angle 4.30130 ( 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 177 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 0.340 Fit side-chains REVERT: R 297 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7201 (mt-10) REVERT: A 315 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7377 (m-30) REVERT: A 329 THR cc_start: 0.7351 (OUTLIER) cc_final: 0.7017 (p) REVERT: B 153 ASP cc_start: 0.8043 (m-30) cc_final: 0.7741 (m-30) REVERT: B 247 ASP cc_start: 0.7880 (t0) cc_final: 0.7559 (t0) REVERT: E 198 SER cc_start: 0.8977 (m) cc_final: 0.8708 (p) outliers start: 28 outliers final: 22 residues processed: 166 average time/residue: 0.1082 time to fit residues: 24.2120 Evaluate side-chains 171 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 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 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 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 218 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.9980 chunk 101 optimal weight: 0.0020 chunk 88 optimal weight: 10.0000 chunk 89 optimal weight: 0.2980 chunk 28 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.185043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.145105 restraints weight = 10430.814| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.31 r_work: 0.3289 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9276 Z= 0.096 Angle : 0.488 9.822 12569 Z= 0.251 Chirality : 0.041 0.225 1442 Planarity : 0.003 0.030 1563 Dihedral : 4.780 35.592 1465 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.53 % Allowed : 13.07 % Favored : 84.40 % 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 aren not related in a simple way. whole: 1.10 (0.25), residues: 1129 helix: 2.47 (0.25), residues: 409 sheet: -0.16 (0.28), residues: 304 loop : -0.27 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.016 0.001 TYR R 119 PHE 0.010 0.001 PHE A 189 TRP 0.008 0.001 TRP B 63 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 9275) covalent geometry : angle 0.48790 (12567) SS BOND : bond 0.00439 ( 1) SS BOND : angle 1.88017 ( 2) hydrogen bonds : bond 0.03231 ( 445) hydrogen bonds : angle 4.17820 ( 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 179 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.355 Fit side-chains REVERT: R 62 ILE cc_start: 0.6353 (mm) cc_final: 0.6045 (tt) REVERT: R 297 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7157 (mt-10) REVERT: A 315 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7350 (m-30) REVERT: A 329 THR cc_start: 0.7281 (OUTLIER) cc_final: 0.6991 (p) REVERT: B 19 ARG cc_start: 0.6477 (ttp-170) cc_final: 0.5604 (mtm180) REVERT: B 153 ASP cc_start: 0.8010 (m-30) cc_final: 0.7731 (m-30) REVERT: B 247 ASP cc_start: 0.7919 (t0) cc_final: 0.7607 (t0) outliers start: 25 outliers final: 19 residues processed: 169 average time/residue: 0.0958 time to fit residues: 21.8856 Evaluate side-chains 170 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 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 269 ASN 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 100 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.179128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.133855 restraints weight = 10634.113| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.52 r_work: 0.3428 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9276 Z= 0.207 Angle : 0.589 10.913 12569 Z= 0.302 Chirality : 0.044 0.223 1442 Planarity : 0.003 0.031 1563 Dihedral : 5.335 35.229 1465 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.23 % Allowed : 13.68 % Favored : 84.09 % 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 aren not related in a simple way. whole: 0.86 (0.25), residues: 1129 helix: 2.20 (0.25), residues: 404 sheet: -0.29 (0.28), residues: 308 loop : -0.28 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 257 TYR 0.012 0.002 TYR R 140 PHE 0.015 0.002 PHE E 27 TRP 0.014 0.002 TRP R 221 HIS 0.005 0.002 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 9275) covalent geometry : angle 0.58838 (12567) SS BOND : bond 0.00361 ( 1) SS BOND : angle 2.71361 ( 2) hydrogen bonds : bond 0.04141 ( 445) hydrogen bonds : angle 4.46721 ( 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 171 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.263 Fit side-chains REVERT: R 297 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7227 (mt-10) REVERT: R 328 ILE cc_start: 0.8639 (tt) cc_final: 0.8407 (tt) REVERT: A 315 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7554 (m-30) REVERT: A 329 THR cc_start: 0.7418 (OUTLIER) cc_final: 0.7111 (p) REVERT: B 19 ARG cc_start: 0.6590 (ttp-170) cc_final: 0.5776 (mtm180) REVERT: B 153 ASP cc_start: 0.8362 (m-30) cc_final: 0.7995 (m-30) REVERT: B 247 ASP cc_start: 0.8042 (t0) cc_final: 0.7778 (t0) REVERT: B 262 MET cc_start: 0.8259 (mtp) cc_final: 0.8043 (mtp) REVERT: B 334 SER cc_start: 0.8696 (m) cc_final: 0.8354 (t) REVERT: E 161 ARG cc_start: 0.7056 (tpp-160) cc_final: 0.6839 (tpp-160) REVERT: E 179 LEU cc_start: 0.8497 (tt) cc_final: 0.8294 (tp) REVERT: E 198 SER cc_start: 0.8991 (m) cc_final: 0.8757 (p) outliers start: 22 outliers final: 20 residues processed: 163 average time/residue: 0.1043 time to fit residues: 22.7194 Evaluate side-chains 167 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 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 269 ASN 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 70 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 122 ASN A 269 ASN E 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.180984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.141213 restraints weight = 10462.649| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.36 r_work: 0.3446 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9276 Z= 0.143 Angle : 0.539 10.852 12569 Z= 0.276 Chirality : 0.042 0.223 1442 Planarity : 0.003 0.029 1563 Dihedral : 5.194 34.589 1465 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.43 % Allowed : 13.78 % Favored : 83.79 % 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 aren not related in a simple way. whole: 0.89 (0.25), residues: 1129 helix: 2.24 (0.25), residues: 405 sheet: -0.29 (0.28), residues: 302 loop : -0.29 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 134 TYR 0.016 0.001 TYR R 119 PHE 0.011 0.001 PHE E 27 TRP 0.009 0.001 TRP B 99 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9275) covalent geometry : angle 0.53839 (12567) SS BOND : bond 0.00443 ( 1) SS BOND : angle 2.37156 ( 2) hydrogen bonds : bond 0.03694 ( 445) hydrogen bonds : angle 4.35072 ( 1278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2324.74 seconds wall clock time: 40 minutes 27.87 seconds (2427.87 seconds total)