Starting phenix.real_space_refine on Thu Jul 2 10:33:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22bj_68152/07_2026/22bj_68152.cif Found real_map, /net/cci-nas-00/data/ceres_data/22bj_68152/07_2026/22bj_68152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/22bj_68152/07_2026/22bj_68152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22bj_68152/07_2026/22bj_68152.map" model { file = "/net/cci-nas-00/data/ceres_data/22bj_68152/07_2026/22bj_68152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22bj_68152/07_2026/22bj_68152.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.031 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: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 37 5.16 5 C 5364 2.51 5 N 1358 2.21 5 O 1321 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8084 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 2016 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 4, 'TRANS': 243} Chain breaks: 1 Chain: "B" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 2016 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 4, 'TRANS': 243} Chain breaks: 1 Chain: "C" Number of atoms: 2027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2027 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 4, 'TRANS': 244} Chain breaks: 1 Chain: "D" Number of atoms: 2021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2021 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 6, 'TRANS': 244} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' K': 3} Chain breaks: 3 Time building chain proxies: 1.74, per 1000 atoms: 0.22 Number of scatterers: 8084 At special positions: 0 Unit cell: (81.432, 118.872, 124.488, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 4 19.00 S 37 16.00 O 1321 8.00 N 1358 7.00 C 5364 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.54 Conformation dependent library (CDL) restraints added in 373.9 milliseconds 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1840 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 0 sheets defined 88.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 71 through 87 removed outlier: 3.757A pdb=" N ARG A 75 " --> pdb=" O ASN A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 92 through 115 removed outlier: 3.749A pdb=" N HIS A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE A 115 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 148 removed outlier: 3.571A pdb=" N GLY A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 156 through 165 removed outlier: 3.933A pdb=" N LEU A 161 " --> pdb=" O TRP A 157 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A 163 " --> pdb=" O GLY A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 184 Processing helix chain 'A' and resid 195 through 203 removed outlier: 3.645A pdb=" N ARG A 198 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER A 199 " --> pdb=" O ALA A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 removed outlier: 3.701A pdb=" N MET A 208 " --> pdb=" O GLN A 204 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET A 211 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 228 Processing helix chain 'A' and resid 228 through 255 Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 287 through 306 removed outlier: 3.845A pdb=" N LEU A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 328 removed outlier: 3.506A pdb=" N GLY A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS A 328 " --> pdb=" O HIS A 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 86 Processing helix chain 'B' and resid 91 through 115 removed outlier: 4.322A pdb=" N TYR B 95 " --> pdb=" O TRP B 91 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 148 removed outlier: 3.642A pdb=" N GLY B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 154 removed outlier: 5.012A pdb=" N CYS B 152 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ARG B 153 " --> pdb=" O CYS B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 removed outlier: 3.659A pdb=" N GLY B 159 " --> pdb=" O ARG B 155 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU B 161 " --> pdb=" O TRP B 157 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS B 162 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 184 removed outlier: 3.798A pdb=" N LEU B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 184 " --> pdb=" O ILE B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 203 removed outlier: 3.519A pdb=" N ARG B 198 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE B 202 " --> pdb=" O SER B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 212 removed outlier: 3.881A pdb=" N MET B 208 " --> pdb=" O GLN B 204 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP B 212 " --> pdb=" O MET B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 228 removed outlier: 3.711A pdb=" N VAL B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 255 Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 287 through 306 removed outlier: 3.739A pdb=" N ILE B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE B 304 " --> pdb=" O ILE B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 328 removed outlier: 3.782A pdb=" N HIS B 328 " --> pdb=" O HIS B 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 87 Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'C' and resid 92 through 114 removed outlier: 3.669A pdb=" N HIS C 96 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 148 removed outlier: 3.880A pdb=" N GLY C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C 128 " --> pdb=" O GLY C 124 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR C 141 " --> pdb=" O PHE C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 155 removed outlier: 5.189A pdb=" N CYS C 152 " --> pdb=" O GLY C 149 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG C 153 " --> pdb=" O CYS C 150 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG C 155 " --> pdb=" O CYS C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 164 removed outlier: 4.276A pdb=" N LEU C 161 " --> pdb=" O TRP C 157 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS C 162 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 163 " --> pdb=" O GLY C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 184 removed outlier: 3.615A pdb=" N ILE C 173 " --> pdb=" O CYS C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 203 Processing helix chain 'C' and resid 204 through 210 removed outlier: 3.660A pdb=" N MET C 208 " --> pdb=" O GLN C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 214 removed outlier: 6.622A pdb=" N ARG C 214 " --> pdb=" O MET C 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 211 through 214' Processing helix chain 'C' and resid 215 through 226 Processing helix chain 'C' and resid 228 through 255 Processing helix chain 'C' and resid 263 through 276 Processing helix chain 'C' and resid 287 through 306 removed outlier: 3.873A pdb=" N LEU C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE C 300 " --> pdb=" O THR C 296 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 327 Processing helix chain 'D' and resid 104 through 117 removed outlier: 4.333A pdb=" N LEU D 110 " --> pdb=" O ARG D 106 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU D 115 " --> pdb=" O ILE D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 143 removed outlier: 4.135A pdb=" N LEU D 124 " --> pdb=" O GLY D 120 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR D 125 " --> pdb=" O TRP D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 177 removed outlier: 3.860A pdb=" N TRP D 155 " --> pdb=" O VAL D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 180 No H-bonds generated for 'chain 'D' and resid 178 through 180' Processing helix chain 'D' and resid 186 through 193 removed outlier: 4.246A pdb=" N ARG D 190 " --> pdb=" O GLY D 186 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 210 Processing helix chain 'D' and resid 222 through 227 Processing helix chain 'D' and resid 230 through 239 removed outlier: 4.047A pdb=" N ILE D 234 " --> pdb=" O ARG D 230 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET D 237 " --> pdb=" O GLN D 233 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 257 Processing helix chain 'D' and resid 257 through 282 Processing helix chain 'D' and resid 302 through 315 Processing helix chain 'D' and resid 326 through 345 removed outlier: 3.603A pdb=" N LEU D 338 " --> pdb=" O ALA D 334 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE D 339 " --> pdb=" O THR D 335 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER D 342 " --> pdb=" O LEU D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 366 597 hydrogen bonds defined for protein. 1743 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: 0.89 Time building geometry restraints manager: 0.77 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: 2440 1.34 - 1.46: 1958 1.46 - 1.58: 3846 1.58 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 8294 Sorted by residual: bond pdb=" N ILE D 107 " pdb=" CA ILE D 107 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.63e+00 bond pdb=" N ARG D 106 " pdb=" CA ARG D 106 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.20e-02 6.94e+03 6.04e+00 bond pdb=" N TYR D 104 " pdb=" CA TYR D 104 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.84e+00 bond pdb=" N GLN D 108 " pdb=" CA GLN D 108 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.31e+00 bond pdb=" N ARG D 227 " pdb=" CA ARG D 227 " ideal model delta sigma weight residual 1.457 1.487 -0.029 1.29e-02 6.01e+03 5.21e+00 ... (remaining 8289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 10856 1.02 - 2.04: 270 2.04 - 3.06: 85 3.06 - 4.08: 9 4.08 - 5.09: 10 Bond angle restraints: 11230 Sorted by residual: angle pdb=" N ARG B 213 " pdb=" CA ARG B 213 " pdb=" C ARG B 213 " ideal model delta sigma weight residual 108.67 113.48 -4.81 1.55e+00 4.16e-01 9.65e+00 angle pdb=" CA ARG A 210 " pdb=" C ARG A 210 " pdb=" O ARG A 210 " ideal model delta sigma weight residual 120.82 117.67 3.15 1.05e+00 9.07e-01 9.02e+00 angle pdb=" O ILE D 107 " pdb=" C ILE D 107 " pdb=" N GLN D 108 " ideal model delta sigma weight residual 121.83 124.51 -2.68 1.03e+00 9.43e-01 6.77e+00 angle pdb=" N TYR D 104 " pdb=" CA TYR D 104 " pdb=" C TYR D 104 " ideal model delta sigma weight residual 111.07 108.37 2.70 1.07e+00 8.73e-01 6.36e+00 angle pdb=" CA ARG D 106 " pdb=" C ARG D 106 " pdb=" O ARG D 106 " ideal model delta sigma weight residual 120.90 118.20 2.70 1.07e+00 8.73e-01 6.35e+00 ... (remaining 11225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 4360 17.75 - 35.49: 307 35.49 - 53.24: 56 53.24 - 70.98: 16 70.98 - 88.73: 6 Dihedral angle restraints: 4745 sinusoidal: 1867 harmonic: 2878 Sorted by residual: dihedral pdb=" CD ARG D 227 " pdb=" NE ARG D 227 " pdb=" CZ ARG D 227 " pdb=" NH1 ARG D 227 " ideal model delta sinusoidal sigma weight residual 0.00 85.32 -85.32 1 1.00e+01 1.00e-02 8.82e+01 dihedral pdb=" CD ARG A 210 " pdb=" NE ARG A 210 " pdb=" CZ ARG A 210 " pdb=" NH1 ARG A 210 " ideal model delta sinusoidal sigma weight residual 0.00 -75.43 75.43 1 1.00e+01 1.00e-02 7.18e+01 dihedral pdb=" CD ARG D 105 " pdb=" NE ARG D 105 " pdb=" CZ ARG D 105 " pdb=" NH1 ARG D 105 " ideal model delta sinusoidal sigma weight residual 0.00 -58.94 58.94 1 1.00e+01 1.00e-02 4.65e+01 ... (remaining 4742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 920 0.037 - 0.074: 284 0.074 - 0.112: 35 0.112 - 0.149: 12 0.149 - 0.186: 1 Chirality restraints: 1252 Sorted by residual: chirality pdb=" CA ILE D 107 " pdb=" N ILE D 107 " pdb=" C ILE D 107 " pdb=" CB ILE D 107 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.63e-01 chirality pdb=" CG LEU D 235 " pdb=" CB LEU D 235 " pdb=" CD1 LEU D 235 " pdb=" CD2 LEU D 235 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA THR C 277 " pdb=" N THR C 277 " pdb=" C THR C 277 " pdb=" CB THR C 277 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 1249 not shown) Planarity restraints: 1353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 227 " -1.101 9.50e-02 1.11e+02 4.93e-01 1.47e+02 pdb=" NE ARG D 227 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG D 227 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG D 227 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG D 227 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 210 " 1.067 9.50e-02 1.11e+02 4.78e-01 1.38e+02 pdb=" NE ARG A 210 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG A 210 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 210 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 210 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 105 " -0.941 9.50e-02 1.11e+02 4.22e-01 1.08e+02 pdb=" NE ARG D 105 " 0.057 2.00e-02 2.50e+03 pdb=" CZ ARG D 105 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG D 105 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG D 105 " -0.024 2.00e-02 2.50e+03 ... (remaining 1350 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.80: 2121 2.80 - 3.38: 9188 3.38 - 3.97: 14927 3.97 - 4.55: 21418 4.55 - 5.14: 30027 Nonbonded interactions: 77681 Sorted by model distance: nonbonded pdb=" OG1 THR A 274 " pdb=" OH TYR B 280 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR A 280 " pdb=" OG1 THR D 313 " model vdw 2.253 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" OH TYR C 280 " model vdw 2.269 3.040 nonbonded pdb=" O SER C 110 " pdb=" OG SER C 113 " model vdw 2.302 3.040 nonbonded pdb=" O LEU C 272 " pdb=" OG1 THR C 276 " model vdw 2.303 3.040 ... (remaining 77676 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 71 through 328) selection = chain 'B' selection = (chain 'C' and resid 71 through 328) } 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: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.340 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:8.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 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 : 0.002 0.036 8294 Z= 0.141 Angle : 0.439 5.094 11230 Z= 0.261 Chirality : 0.036 0.186 1252 Planarity : 0.025 0.493 1353 Dihedral : 13.190 88.729 2905 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.84 % Allowed : 0.72 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.26), residues: 978 helix: 0.74 (0.18), residues: 782 sheet: None (None), residues: 0 loop : 1.12 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 227 TYR 0.011 0.001 TYR B 82 PHE 0.012 0.001 PHE D 231 TRP 0.018 0.001 TRP B 288 HIS 0.002 0.001 HIS C 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.14 ( 8294) covalent geometry : angle 0.43931 / 0.26 (11230) hydrogen bonds : bond 0.22816 / 14.82 ( 597) hydrogen bonds : angle 7.13481 / 5.19 ( 1743) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 167 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7786 (mmt180) cc_final: 0.7257 (mtm180) REVERT: A 153 ARG cc_start: 0.6449 (tpt90) cc_final: 0.5874 (tpm-80) REVERT: A 174 MET cc_start: 0.8085 (mtm) cc_final: 0.7738 (tmt) REVERT: A 219 LYS cc_start: 0.7269 (mttp) cc_final: 0.7000 (mtpt) REVERT: A 226 TYR cc_start: 0.7798 (t80) cc_final: 0.7545 (t80) REVERT: A 236 TRP cc_start: 0.7133 (m-10) cc_final: 0.6320 (m100) REVERT: B 87 ARG cc_start: 0.7427 (mtt180) cc_final: 0.7155 (mmt90) REVERT: B 89 ARG cc_start: 0.6265 (ppt170) cc_final: 0.6038 (ptm-80) REVERT: B 98 TYR cc_start: 0.6359 (m-10) cc_final: 0.5615 (t80) REVERT: B 110 SER cc_start: 0.6845 (t) cc_final: 0.6608 (p) REVERT: B 120 LYS cc_start: 0.8318 (tptt) cc_final: 0.7884 (mmpt) REVERT: B 214 ARG cc_start: 0.6998 (mmt180) cc_final: 0.6710 (mmt180) REVERT: B 286 GLN cc_start: 0.8265 (mt0) cc_final: 0.8017 (mt0) REVERT: B 287 THR cc_start: 0.7231 (m) cc_final: 0.6682 (p) REVERT: C 87 ARG cc_start: 0.7832 (mmt-90) cc_final: 0.7339 (mmt-90) REVERT: C 89 ARG cc_start: 0.6575 (ttp80) cc_final: 0.6145 (ttp80) REVERT: C 116 LYS cc_start: 0.8273 (ttpt) cc_final: 0.7781 (tptt) REVERT: C 117 GLU cc_start: 0.7949 (tt0) cc_final: 0.7681 (mt-10) REVERT: C 255 LYS cc_start: 0.7914 (tptp) cc_final: 0.7631 (tptm) REVERT: D 103 LYS cc_start: 0.5156 (OUTLIER) cc_final: 0.4552 (mtpp) REVERT: D 190 ARG cc_start: 0.6388 (mtm-85) cc_final: 0.5732 (mmt-90) REVERT: D 265 TRP cc_start: 0.7493 (m-10) cc_final: 0.6935 (m100) REVERT: D 275 SER cc_start: 0.8287 (p) cc_final: 0.8040 (p) REVERT: D 299 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8240 (mt-10) REVERT: D 301 GLU cc_start: 0.7997 (pt0) cc_final: 0.7606 (tt0) REVERT: D 358 LYS cc_start: 0.7524 (ttmt) cc_final: 0.6903 (mmtm) outliers start: 7 outliers final: 5 residues processed: 173 average time/residue: 0.6904 time to fit residues: 125.4720 Evaluate side-chains 138 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 106 ARG Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 330 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN A 286 GLN C 323 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.192597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.108418 restraints weight = 8295.777| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.07 r_work: 0.3117 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8294 Z= 0.205 Angle : 0.549 5.845 11230 Z= 0.297 Chirality : 0.042 0.184 1252 Planarity : 0.005 0.033 1353 Dihedral : 5.626 57.322 1127 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.41 % Allowed : 9.27 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.26), residues: 978 helix: 1.33 (0.18), residues: 776 sheet: None (None), residues: 0 loop : 1.35 (0.46), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 201 TYR 0.015 0.001 TYR A 74 PHE 0.013 0.002 PHE A 137 TRP 0.015 0.002 TRP B 288 HIS 0.003 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 ( 8294) covalent geometry : angle 0.54942 / 0.30 (11230) hydrogen bonds : bond 0.05142 / 3.32 ( 597) hydrogen bonds : angle 4.37387 / 3.17 ( 1743) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7780 (mmt180) cc_final: 0.7176 (mtm180) REVERT: A 153 ARG cc_start: 0.6480 (tpt90) cc_final: 0.5851 (tpm-80) REVERT: A 174 MET cc_start: 0.8051 (mtm) cc_final: 0.7681 (tmt) REVERT: A 236 TRP cc_start: 0.7441 (m-10) cc_final: 0.6643 (m100) REVERT: A 255 LYS cc_start: 0.8154 (tptt) cc_final: 0.7804 (tptp) REVERT: B 84 VAL cc_start: 0.6370 (t) cc_final: 0.5967 (p) REVERT: B 87 ARG cc_start: 0.7726 (mtt180) cc_final: 0.7373 (mmt90) REVERT: B 89 ARG cc_start: 0.6403 (ppt170) cc_final: 0.6151 (ptm-80) REVERT: B 110 SER cc_start: 0.6878 (t) cc_final: 0.6613 (p) REVERT: B 287 THR cc_start: 0.7911 (m) cc_final: 0.7504 (p) REVERT: B 314 SER cc_start: 0.8356 (t) cc_final: 0.8142 (m) REVERT: B 319 LYS cc_start: 0.7405 (ttmt) cc_final: 0.7042 (ttpt) REVERT: C 87 ARG cc_start: 0.8113 (mmt-90) cc_final: 0.7592 (mmt-90) REVERT: C 89 ARG cc_start: 0.6923 (ttp80) cc_final: 0.6454 (ttp80) REVERT: C 116 LYS cc_start: 0.8550 (ttpt) cc_final: 0.8063 (tptt) REVERT: C 117 GLU cc_start: 0.8169 (tt0) cc_final: 0.7797 (mt-10) REVERT: C 165 ARG cc_start: 0.6776 (mtt90) cc_final: 0.6496 (mtm110) REVERT: C 255 LYS cc_start: 0.8196 (tptp) cc_final: 0.7991 (tptm) REVERT: D 255 CYS cc_start: 0.8130 (t) cc_final: 0.7804 (m) REVERT: D 265 TRP cc_start: 0.7586 (m-10) cc_final: 0.6957 (m100) REVERT: D 301 GLU cc_start: 0.8020 (pt0) cc_final: 0.7684 (tt0) REVERT: D 328 GLU cc_start: 0.6358 (mt-10) cc_final: 0.6100 (mp0) outliers start: 20 outliers final: 4 residues processed: 164 average time/residue: 0.6694 time to fit residues: 115.3908 Evaluate side-chains 133 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 129 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain D residue 106 ARG Chi-restraints excluded: chain D residue 330 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 41 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 11 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 92 optimal weight: 0.3980 chunk 63 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 GLN ** C 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.192511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.109427 restraints weight = 8377.120| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.10 r_work: 0.3019 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8294 Z= 0.131 Angle : 0.465 5.243 11230 Z= 0.250 Chirality : 0.038 0.151 1252 Planarity : 0.004 0.034 1353 Dihedral : 4.955 55.807 1115 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Rotamer: Outliers : 1.93 % Allowed : 12.76 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.26), residues: 978 helix: 1.57 (0.18), residues: 779 sheet: None (None), residues: 0 loop : 1.14 (0.45), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 201 TYR 0.015 0.001 TYR B 118 PHE 0.016 0.001 PHE D 130 TRP 0.011 0.001 TRP B 288 HIS 0.005 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 8294) covalent geometry : angle 0.46545 / 0.25 (11230) hydrogen bonds : bond 0.04248 / 2.76 ( 597) hydrogen bonds : angle 3.96824 / 2.86 ( 1743) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7679 (mmt180) cc_final: 0.7070 (mtm180) REVERT: A 153 ARG cc_start: 0.6619 (tpt90) cc_final: 0.6068 (tpm-80) REVERT: A 174 MET cc_start: 0.7917 (mtm) cc_final: 0.7590 (tmt) REVERT: A 236 TRP cc_start: 0.7273 (m-10) cc_final: 0.6545 (m100) REVERT: B 84 VAL cc_start: 0.6126 (t) cc_final: 0.5756 (p) REVERT: B 87 ARG cc_start: 0.7683 (mtt180) cc_final: 0.7323 (mmt90) REVERT: B 89 ARG cc_start: 0.6394 (ppt170) cc_final: 0.6129 (ptm-80) REVERT: B 287 THR cc_start: 0.7626 (m) cc_final: 0.7305 (p) REVERT: B 302 VAL cc_start: 0.7636 (m) cc_final: 0.7326 (t) REVERT: C 89 ARG cc_start: 0.6710 (ttp80) cc_final: 0.6223 (ttp80) REVERT: C 116 LYS cc_start: 0.8467 (ttpt) cc_final: 0.7967 (tptt) REVERT: C 117 GLU cc_start: 0.8092 (tt0) cc_final: 0.7684 (mt-10) REVERT: C 165 ARG cc_start: 0.6738 (mtt90) cc_final: 0.6529 (mtm110) REVERT: C 230 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.7046 (tttm) REVERT: C 255 LYS cc_start: 0.7984 (tptp) cc_final: 0.7781 (tptm) REVERT: D 162 PHE cc_start: 0.6918 (t80) cc_final: 0.6236 (OUTLIER) REVERT: D 237 MET cc_start: 0.7570 (tpp) cc_final: 0.7274 (mmt) REVERT: D 255 CYS cc_start: 0.7920 (t) cc_final: 0.7557 (m) REVERT: D 265 TRP cc_start: 0.7424 (m-10) cc_final: 0.6801 (m100) REVERT: D 275 SER cc_start: 0.7857 (p) cc_final: 0.7647 (p) REVERT: D 301 GLU cc_start: 0.8032 (pt0) cc_final: 0.7809 (tt0) REVERT: D 328 GLU cc_start: 0.6277 (mt-10) cc_final: 0.6011 (mp0) REVERT: D 358 LYS cc_start: 0.7335 (ttmt) cc_final: 0.6678 (tptt) outliers start: 16 outliers final: 5 residues processed: 144 average time/residue: 0.6480 time to fit residues: 98.2320 Evaluate side-chains 134 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 129 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 230 LYS Chi-restraints excluded: chain D residue 106 ARG Chi-restraints excluded: chain D residue 330 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 59 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 76 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 GLN D 367 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.188357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.104312 restraints weight = 8424.629| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.08 r_work: 0.2940 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8294 Z= 0.207 Angle : 0.535 6.514 11230 Z= 0.286 Chirality : 0.041 0.183 1252 Planarity : 0.004 0.037 1353 Dihedral : 5.072 58.897 1115 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.89 % Allowed : 13.24 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.26), residues: 978 helix: 1.40 (0.18), residues: 785 sheet: None (None), residues: 0 loop : 0.94 (0.47), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 155 TYR 0.016 0.001 TYR B 118 PHE 0.012 0.002 PHE B 137 TRP 0.014 0.002 TRP B 288 HIS 0.004 0.001 HIS C 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.21 ( 8294) covalent geometry : angle 0.53524 / 0.29 (11230) hydrogen bonds : bond 0.04642 / 3.00 ( 597) hydrogen bonds : angle 4.10472 / 2.97 ( 1743) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7649 (mmt180) cc_final: 0.6996 (mtm180) REVERT: A 134 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.7090 (pt) REVERT: A 153 ARG cc_start: 0.6812 (tpt90) cc_final: 0.6291 (tpt90) REVERT: A 174 MET cc_start: 0.7989 (mtm) cc_final: 0.7591 (tmt) REVERT: A 198 ARG cc_start: 0.5856 (pmt170) cc_final: 0.5465 (tmt170) REVERT: A 236 TRP cc_start: 0.7376 (m-10) cc_final: 0.6563 (m100) REVERT: B 87 ARG cc_start: 0.7734 (mtt180) cc_final: 0.7351 (mtt-85) REVERT: B 89 ARG cc_start: 0.6398 (ppt170) cc_final: 0.6139 (ptm-80) REVERT: B 287 THR cc_start: 0.7737 (m) cc_final: 0.7364 (p) REVERT: B 322 GLU cc_start: 0.7043 (tt0) cc_final: 0.6515 (pt0) REVERT: B 323 GLN cc_start: 0.7082 (mt0) cc_final: 0.6875 (mt0) REVERT: C 89 ARG cc_start: 0.6577 (ttp80) cc_final: 0.6071 (ttm110) REVERT: C 116 LYS cc_start: 0.8500 (ttpt) cc_final: 0.8019 (tptt) REVERT: C 117 GLU cc_start: 0.7977 (tt0) cc_final: 0.7603 (mt-10) REVERT: C 165 ARG cc_start: 0.6749 (mtt90) cc_final: 0.6471 (mtp-110) REVERT: C 230 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.6874 (tttm) REVERT: D 162 PHE cc_start: 0.6981 (t80) cc_final: 0.6267 (m-10) REVERT: D 265 TRP cc_start: 0.7439 (m-10) cc_final: 0.6781 (m100) REVERT: D 296 MET cc_start: 0.7283 (pmm) cc_final: 0.6918 (pmm) REVERT: D 301 GLU cc_start: 0.8076 (pt0) cc_final: 0.7856 (tt0) REVERT: D 328 GLU cc_start: 0.6299 (OUTLIER) cc_final: 0.5994 (mp0) outliers start: 24 outliers final: 9 residues processed: 138 average time/residue: 0.6893 time to fit residues: 99.8214 Evaluate side-chains 134 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 230 LYS Chi-restraints excluded: chain C residue 260 HIS Chi-restraints excluded: chain D residue 106 ARG Chi-restraints excluded: chain D residue 108 GLN Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 361 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 70 optimal weight: 0.0980 chunk 27 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 89 optimal weight: 0.0870 chunk 44 optimal weight: 0.3980 chunk 91 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 204 GLN ** 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 = 0.4188 r_free = 0.4188 target = 0.193200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.110789 restraints weight = 8475.819| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.10 r_work: 0.3036 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8294 Z= 0.107 Angle : 0.450 6.021 11230 Z= 0.240 Chirality : 0.036 0.165 1252 Planarity : 0.003 0.044 1353 Dihedral : 4.717 59.664 1115 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 1.32 % Allowed : 15.88 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.26), residues: 978 helix: 1.74 (0.18), residues: 783 sheet: None (None), residues: 0 loop : 0.86 (0.46), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 227 TYR 0.011 0.001 TYR A 280 PHE 0.014 0.001 PHE D 130 TRP 0.012 0.001 TRP B 288 HIS 0.004 0.001 HIS C 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 ( 8294) covalent geometry : angle 0.44996 / 0.24 (11230) hydrogen bonds : bond 0.03898 / 2.53 ( 597) hydrogen bonds : angle 3.80356 / 2.74 ( 1743) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7708 (mmt180) cc_final: 0.7075 (mtm180) REVERT: A 134 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7089 (pt) REVERT: A 153 ARG cc_start: 0.6720 (tpt90) cc_final: 0.6185 (tpt90) REVERT: A 174 MET cc_start: 0.7917 (mtm) cc_final: 0.7528 (tmt) REVERT: A 198 ARG cc_start: 0.6019 (pmt170) cc_final: 0.5466 (tmt170) REVERT: A 236 TRP cc_start: 0.7371 (m-10) cc_final: 0.6650 (m100) REVERT: B 87 ARG cc_start: 0.7762 (mtt180) cc_final: 0.7377 (mtt-85) REVERT: B 89 ARG cc_start: 0.6380 (ppt170) cc_final: 0.6091 (ptm-80) REVERT: B 210 ARG cc_start: 0.6953 (ttp-170) cc_final: 0.6748 (ptt180) REVERT: B 287 THR cc_start: 0.7608 (m) cc_final: 0.7276 (p) REVERT: B 302 VAL cc_start: 0.7583 (m) cc_final: 0.7275 (t) REVERT: B 323 GLN cc_start: 0.7177 (mt0) cc_final: 0.6966 (mt0) REVERT: C 89 ARG cc_start: 0.6444 (ttp80) cc_final: 0.5990 (mtm110) REVERT: C 116 LYS cc_start: 0.8478 (ttpt) cc_final: 0.7985 (tptt) REVERT: C 117 GLU cc_start: 0.7997 (tt0) cc_final: 0.7629 (mt-10) REVERT: C 165 ARG cc_start: 0.6766 (mtt90) cc_final: 0.6508 (mtm110) REVERT: C 230 LYS cc_start: 0.7374 (tmtm) cc_final: 0.7008 (tttm) REVERT: D 162 PHE cc_start: 0.6970 (t80) cc_final: 0.6323 (m-10) REVERT: D 265 TRP cc_start: 0.7438 (m-10) cc_final: 0.6783 (m100) REVERT: D 301 GLU cc_start: 0.8109 (pt0) cc_final: 0.7854 (tt0) REVERT: D 328 GLU cc_start: 0.6253 (mt-10) cc_final: 0.5950 (mp0) REVERT: D 358 LYS cc_start: 0.7489 (ttmt) cc_final: 0.6678 (tppt) outliers start: 11 outliers final: 3 residues processed: 139 average time/residue: 0.5470 time to fit residues: 80.0755 Evaluate side-chains 124 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 361 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 96 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 204 GLN ** 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 = 0.4172 r_free = 0.4172 target = 0.191597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.108423 restraints weight = 8390.973| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.09 r_work: 0.3002 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8294 Z= 0.129 Angle : 0.464 5.831 11230 Z= 0.246 Chirality : 0.037 0.143 1252 Planarity : 0.004 0.036 1353 Dihedral : 4.453 58.329 1111 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 1.32 % Allowed : 17.09 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.27), residues: 978 helix: 1.84 (0.18), residues: 782 sheet: None (None), residues: 0 loop : 0.91 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 227 TYR 0.011 0.001 TYR A 280 PHE 0.019 0.001 PHE D 130 TRP 0.013 0.001 TRP B 288 HIS 0.003 0.001 HIS C 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 8294) covalent geometry : angle 0.46357 / 0.25 (11230) hydrogen bonds : bond 0.03968 / 2.58 ( 597) hydrogen bonds : angle 3.78576 / 2.74 ( 1743) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7627 (mmt180) cc_final: 0.6947 (mtm180) REVERT: A 134 ILE cc_start: 0.7617 (OUTLIER) cc_final: 0.7113 (pt) REVERT: A 153 ARG cc_start: 0.6703 (tpt90) cc_final: 0.6191 (tpt90) REVERT: A 174 MET cc_start: 0.7928 (mtm) cc_final: 0.7564 (tmt) REVERT: A 198 ARG cc_start: 0.6038 (pmt170) cc_final: 0.5532 (tmt170) REVERT: A 219 LYS cc_start: 0.7458 (mtpt) cc_final: 0.7245 (mttt) REVERT: A 236 TRP cc_start: 0.7312 (m-10) cc_final: 0.6595 (m100) REVERT: B 84 VAL cc_start: 0.6342 (t) cc_final: 0.6009 (p) REVERT: B 87 ARG cc_start: 0.7788 (mtt180) cc_final: 0.7393 (mtt-85) REVERT: B 89 ARG cc_start: 0.6391 (ppt170) cc_final: 0.6068 (ptm-80) REVERT: B 210 ARG cc_start: 0.6902 (ttp-170) cc_final: 0.6693 (ptt180) REVERT: B 287 THR cc_start: 0.7652 (m) cc_final: 0.7309 (p) REVERT: B 302 VAL cc_start: 0.7602 (m) cc_final: 0.7296 (t) REVERT: B 323 GLN cc_start: 0.7166 (mt0) cc_final: 0.6941 (mt0) REVERT: C 89 ARG cc_start: 0.6431 (ttp80) cc_final: 0.6009 (mtm110) REVERT: C 116 LYS cc_start: 0.8486 (ttpt) cc_final: 0.8015 (tptt) REVERT: C 117 GLU cc_start: 0.7987 (tt0) cc_final: 0.7623 (mt-10) REVERT: C 230 LYS cc_start: 0.7392 (tmtm) cc_final: 0.7040 (tttm) REVERT: D 162 PHE cc_start: 0.6967 (t80) cc_final: 0.6350 (m-10) REVERT: D 255 CYS cc_start: 0.7901 (t) cc_final: 0.7494 (m) REVERT: D 265 TRP cc_start: 0.7461 (m-10) cc_final: 0.6779 (m100) REVERT: D 301 GLU cc_start: 0.8094 (pt0) cc_final: 0.7861 (tt0) REVERT: D 328 GLU cc_start: 0.6247 (OUTLIER) cc_final: 0.5948 (mp0) REVERT: D 358 LYS cc_start: 0.7470 (ttmt) cc_final: 0.6711 (tppt) outliers start: 11 outliers final: 5 residues processed: 138 average time/residue: 0.5705 time to fit residues: 82.8220 Evaluate side-chains 131 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 361 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 204 GLN ** 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 = 0.4219 r_free = 0.4219 target = 0.192073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.109324 restraints weight = 8394.509| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.08 r_work: 0.3146 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8294 Z= 0.135 Angle : 0.475 9.842 11230 Z= 0.247 Chirality : 0.037 0.149 1252 Planarity : 0.004 0.034 1353 Dihedral : 4.437 57.332 1111 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 2.17 % Allowed : 16.49 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.26), residues: 978 helix: 1.87 (0.18), residues: 782 sheet: None (None), residues: 0 loop : 1.02 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 201 TYR 0.010 0.001 TYR A 74 PHE 0.019 0.001 PHE D 130 TRP 0.017 0.001 TRP B 288 HIS 0.004 0.001 HIS C 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 8294) covalent geometry : angle 0.47460 / 0.25 (11230) hydrogen bonds : bond 0.03950 / 2.57 ( 597) hydrogen bonds : angle 3.76422 / 2.72 ( 1743) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7721 (mmt180) cc_final: 0.7058 (mtm180) REVERT: A 134 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7043 (pt) REVERT: A 153 ARG cc_start: 0.6765 (tpt90) cc_final: 0.6256 (tpt90) REVERT: A 155 ARG cc_start: 0.3495 (tpm170) cc_final: 0.3181 (tpm170) REVERT: A 174 MET cc_start: 0.7953 (mtm) cc_final: 0.7587 (tmt) REVERT: A 198 ARG cc_start: 0.6130 (pmt170) cc_final: 0.5564 (tmt170) REVERT: A 219 LYS cc_start: 0.7630 (mtpt) cc_final: 0.7409 (mttt) REVERT: A 236 TRP cc_start: 0.7465 (m-10) cc_final: 0.6745 (m100) REVERT: A 327 LYS cc_start: 0.7336 (mmtp) cc_final: 0.6961 (mtpt) REVERT: B 84 VAL cc_start: 0.6528 (t) cc_final: 0.6184 (p) REVERT: B 87 ARG cc_start: 0.7788 (mtt180) cc_final: 0.7239 (mtm180) REVERT: B 89 ARG cc_start: 0.6380 (ppt170) cc_final: 0.6074 (ptm-80) REVERT: B 210 ARG cc_start: 0.7030 (ttp-170) cc_final: 0.6826 (ptt180) REVERT: B 211 MET cc_start: 0.7191 (ttp) cc_final: 0.6820 (mtm) REVERT: B 302 VAL cc_start: 0.7815 (m) cc_final: 0.7496 (t) REVERT: B 323 GLN cc_start: 0.7334 (mt0) cc_final: 0.7096 (mt0) REVERT: C 89 ARG cc_start: 0.6511 (ttp80) cc_final: 0.6093 (mtm110) REVERT: C 116 LYS cc_start: 0.8540 (ttpt) cc_final: 0.8085 (tptt) REVERT: C 117 GLU cc_start: 0.8011 (tt0) cc_final: 0.7641 (mt-10) REVERT: C 198 ARG cc_start: 0.6789 (ttp80) cc_final: 0.6510 (ttp80) REVERT: C 230 LYS cc_start: 0.7526 (tmtm) cc_final: 0.7164 (tttm) REVERT: C 257 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8018 (mt-10) REVERT: D 162 PHE cc_start: 0.7030 (t80) cc_final: 0.6389 (m-10) REVERT: D 240 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.6697 (ttm) REVERT: D 265 TRP cc_start: 0.7604 (m-10) cc_final: 0.6907 (m100) REVERT: D 301 GLU cc_start: 0.8158 (pt0) cc_final: 0.7913 (tt0) REVERT: D 328 GLU cc_start: 0.6525 (OUTLIER) cc_final: 0.6249 (mp0) REVERT: D 358 LYS cc_start: 0.7645 (ttmt) cc_final: 0.6914 (tppt) outliers start: 18 outliers final: 7 residues processed: 139 average time/residue: 0.5570 time to fit residues: 81.6206 Evaluate side-chains 135 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain D residue 240 MET Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 361 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 76 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 78 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 92 optimal weight: 0.0870 chunk 37 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 61 optimal weight: 0.0870 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.194090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.112926 restraints weight = 8358.152| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.08 r_work: 0.3143 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8294 Z= 0.104 Angle : 0.449 8.865 11230 Z= 0.232 Chirality : 0.036 0.144 1252 Planarity : 0.003 0.033 1353 Dihedral : 4.301 57.008 1111 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Rotamer: Outliers : 1.68 % Allowed : 16.73 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.27), residues: 978 helix: 2.02 (0.18), residues: 783 sheet: None (None), residues: 0 loop : 0.96 (0.47), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 201 TYR 0.009 0.001 TYR A 74 PHE 0.018 0.001 PHE D 130 TRP 0.020 0.001 TRP B 288 HIS 0.004 0.001 HIS C 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 8294) covalent geometry : angle 0.44891 / 0.23 (11230) hydrogen bonds : bond 0.03645 / 2.38 ( 597) hydrogen bonds : angle 3.62620 / 2.63 ( 1743) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7878 (mmt180) cc_final: 0.7156 (mtm180) REVERT: A 134 ILE cc_start: 0.7604 (OUTLIER) cc_final: 0.7105 (pt) REVERT: A 153 ARG cc_start: 0.6754 (tpt90) cc_final: 0.6214 (tpt90) REVERT: A 174 MET cc_start: 0.7979 (mtm) cc_final: 0.7594 (tmt) REVERT: A 198 ARG cc_start: 0.6131 (pmt170) cc_final: 0.5594 (tmt170) REVERT: A 219 LYS cc_start: 0.7814 (mtpt) cc_final: 0.7587 (mttt) REVERT: A 236 TRP cc_start: 0.7570 (m-10) cc_final: 0.6892 (m100) REVERT: A 327 LYS cc_start: 0.7387 (mmtp) cc_final: 0.7007 (mtmt) REVERT: B 84 VAL cc_start: 0.6543 (t) cc_final: 0.6165 (p) REVERT: B 87 ARG cc_start: 0.7841 (mtt180) cc_final: 0.7128 (mtm110) REVERT: B 89 ARG cc_start: 0.6331 (ppt170) cc_final: 0.6050 (ptm-80) REVERT: B 302 VAL cc_start: 0.7716 (m) cc_final: 0.7408 (t) REVERT: B 323 GLN cc_start: 0.7479 (mt0) cc_final: 0.7234 (mt0) REVERT: C 89 ARG cc_start: 0.6534 (ttp80) cc_final: 0.6075 (mtm110) REVERT: C 116 LYS cc_start: 0.8581 (ttpt) cc_final: 0.8114 (tptt) REVERT: C 117 GLU cc_start: 0.8080 (tt0) cc_final: 0.7752 (mt-10) REVERT: C 230 LYS cc_start: 0.7614 (tmtm) cc_final: 0.7258 (tttm) REVERT: D 240 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6817 (mtp) REVERT: D 255 CYS cc_start: 0.8175 (t) cc_final: 0.7799 (m) REVERT: D 265 TRP cc_start: 0.7737 (m-10) cc_final: 0.7044 (m100) REVERT: D 328 GLU cc_start: 0.6554 (mt-10) cc_final: 0.6297 (mp0) REVERT: D 358 LYS cc_start: 0.7755 (ttmt) cc_final: 0.7011 (tppt) outliers start: 14 outliers final: 5 residues processed: 135 average time/residue: 0.6011 time to fit residues: 85.3289 Evaluate side-chains 128 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain D residue 240 MET Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain D residue 361 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 33 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 12 optimal weight: 0.3980 chunk 90 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 204 GLN ** 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 = 0.4226 r_free = 0.4226 target = 0.193050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.111236 restraints weight = 8401.512| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.08 r_work: 0.3115 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8294 Z= 0.117 Angle : 0.463 9.107 11230 Z= 0.240 Chirality : 0.037 0.143 1252 Planarity : 0.003 0.032 1353 Dihedral : 4.343 56.278 1111 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 1.44 % Allowed : 17.57 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.67 (0.27), residues: 978 helix: 2.03 (0.18), residues: 782 sheet: None (None), residues: 0 loop : 0.89 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 201 TYR 0.010 0.001 TYR A 280 PHE 0.015 0.001 PHE D 130 TRP 0.022 0.001 TRP B 288 HIS 0.003 0.001 HIS C 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 8294) covalent geometry : angle 0.46273 / 0.24 (11230) hydrogen bonds : bond 0.03763 / 2.45 ( 597) hydrogen bonds : angle 3.64154 / 2.63 ( 1743) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7817 (mmt180) cc_final: 0.7097 (mtm180) REVERT: A 134 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.7092 (pt) REVERT: A 153 ARG cc_start: 0.6807 (tpt90) cc_final: 0.6255 (tpt90) REVERT: A 174 MET cc_start: 0.7990 (mtm) cc_final: 0.7603 (tmt) REVERT: A 198 ARG cc_start: 0.6108 (pmt170) cc_final: 0.5604 (tmt170) REVERT: A 219 LYS cc_start: 0.7818 (mtpt) cc_final: 0.7580 (mttt) REVERT: A 236 TRP cc_start: 0.7606 (m-10) cc_final: 0.6934 (m100) REVERT: A 257 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8087 (mm-30) REVERT: A 327 LYS cc_start: 0.7403 (mmtp) cc_final: 0.6978 (mtmt) REVERT: B 84 VAL cc_start: 0.6585 (t) cc_final: 0.6247 (p) REVERT: B 87 ARG cc_start: 0.7885 (mtt180) cc_final: 0.7084 (mtm110) REVERT: B 89 ARG cc_start: 0.6345 (ppt170) cc_final: 0.6062 (ptm-80) REVERT: B 302 VAL cc_start: 0.7739 (m) cc_final: 0.7438 (t) REVERT: B 323 GLN cc_start: 0.7463 (mt0) cc_final: 0.7214 (mt0) REVERT: C 89 ARG cc_start: 0.6341 (ttp80) cc_final: 0.5954 (mtm110) REVERT: C 116 LYS cc_start: 0.8586 (ttpt) cc_final: 0.8118 (tptt) REVERT: C 117 GLU cc_start: 0.8082 (tt0) cc_final: 0.7741 (mt-10) REVERT: D 240 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.6844 (mtm) REVERT: D 255 CYS cc_start: 0.8184 (t) cc_final: 0.7817 (m) REVERT: D 265 TRP cc_start: 0.7746 (m-10) cc_final: 0.7061 (m100) REVERT: D 328 GLU cc_start: 0.6535 (mt-10) cc_final: 0.6284 (mp0) REVERT: D 358 LYS cc_start: 0.7734 (ttmt) cc_final: 0.6912 (tppt) REVERT: D 361 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7241 (pt0) outliers start: 12 outliers final: 5 residues processed: 129 average time/residue: 0.5883 time to fit residues: 79.8987 Evaluate side-chains 129 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain D residue 240 MET Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain D residue 361 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 32 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 204 GLN ** 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 = 0.4216 r_free = 0.4216 target = 0.192038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.109754 restraints weight = 8310.895| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.07 r_work: 0.3152 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8294 Z= 0.132 Angle : 0.475 10.165 11230 Z= 0.248 Chirality : 0.037 0.140 1252 Planarity : 0.003 0.033 1353 Dihedral : 4.402 56.294 1111 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 1.56 % Allowed : 17.57 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.27), residues: 978 helix: 1.99 (0.18), residues: 784 sheet: None (None), residues: 0 loop : 0.97 (0.47), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 201 TYR 0.010 0.001 TYR A 74 PHE 0.014 0.001 PHE D 231 TRP 0.026 0.001 TRP B 288 HIS 0.003 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 8294) covalent geometry : angle 0.47451 / 0.25 (11230) hydrogen bonds : bond 0.03892 / 2.54 ( 597) hydrogen bonds : angle 3.69139 / 2.67 ( 1743) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7778 (mmt180) cc_final: 0.7051 (mtm180) REVERT: A 134 ILE cc_start: 0.7538 (OUTLIER) cc_final: 0.7031 (pt) REVERT: A 153 ARG cc_start: 0.6891 (tpt90) cc_final: 0.6326 (tpt90) REVERT: A 174 MET cc_start: 0.7969 (mtm) cc_final: 0.7587 (tmt) REVERT: A 198 ARG cc_start: 0.6085 (pmt170) cc_final: 0.5533 (tmt170) REVERT: A 219 LYS cc_start: 0.7643 (mtpt) cc_final: 0.7409 (mttt) REVERT: A 236 TRP cc_start: 0.7476 (m-10) cc_final: 0.6800 (m100) REVERT: A 327 LYS cc_start: 0.7406 (mmtp) cc_final: 0.6988 (mtmt) REVERT: B 84 VAL cc_start: 0.6513 (t) cc_final: 0.6169 (p) REVERT: B 87 ARG cc_start: 0.7907 (mtt180) cc_final: 0.7080 (mtm110) REVERT: B 89 ARG cc_start: 0.6254 (ppt170) cc_final: 0.5963 (ptm-80) REVERT: B 302 VAL cc_start: 0.7792 (m) cc_final: 0.7479 (t) REVERT: C 89 ARG cc_start: 0.6204 (ttp80) cc_final: 0.5866 (mtm110) REVERT: C 116 LYS cc_start: 0.8544 (ttpt) cc_final: 0.8092 (tptt) REVERT: C 117 GLU cc_start: 0.8014 (tt0) cc_final: 0.7658 (mt-10) REVERT: C 214 ARG cc_start: 0.6968 (mpt180) cc_final: 0.6254 (mtm110) REVERT: D 200 MET cc_start: 0.7520 (mtm) cc_final: 0.6822 (mmm) REVERT: D 240 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.6768 (mtp) REVERT: D 255 CYS cc_start: 0.8084 (t) cc_final: 0.7669 (m) REVERT: D 328 GLU cc_start: 0.6535 (mt-10) cc_final: 0.6258 (mp0) REVERT: D 358 LYS cc_start: 0.7624 (ttmt) cc_final: 0.6874 (tppt) outliers start: 13 outliers final: 7 residues processed: 130 average time/residue: 0.6409 time to fit residues: 87.5511 Evaluate side-chains 131 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 260 HIS Chi-restraints excluded: chain D residue 240 MET Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 361 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 3 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 76 optimal weight: 0.0980 chunk 63 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 204 GLN ** 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 = 0.4223 r_free = 0.4223 target = 0.192735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.111089 restraints weight = 8330.241| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.07 r_work: 0.3172 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8294 Z= 0.117 Angle : 0.459 9.535 11230 Z= 0.239 Chirality : 0.037 0.135 1252 Planarity : 0.003 0.032 1353 Dihedral : 4.333 56.175 1111 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 1.20 % Allowed : 17.93 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.74 (0.27), residues: 978 helix: 2.05 (0.18), residues: 786 sheet: None (None), residues: 0 loop : 1.04 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 201 TYR 0.010 0.001 TYR A 74 PHE 0.015 0.001 PHE D 130 TRP 0.027 0.001 TRP B 288 HIS 0.003 0.001 HIS C 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 8294) covalent geometry : angle 0.45948 / 0.24 (11230) hydrogen bonds : bond 0.03745 / 2.44 ( 597) hydrogen bonds : angle 3.62657 / 2.63 ( 1743) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4258.18 seconds wall clock time: 72 minutes 57.68 seconds (4377.68 seconds total)