Starting phenix.real_space_refine on Wed Jul 1 22:30:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7u10_26273/07_2026/7u10_26273.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u10_26273/07_2026/7u10_26273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7u10_26273/07_2026/7u10_26273.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7u10_26273/07_2026/7u10_26273.cif" model { file = "/net/cci-nas-00/data/ceres_data/7u10_26273/07_2026/7u10_26273.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u10_26273/07_2026/7u10_26273.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u10_26273/07_2026/7u10_26273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u10_26273/07_2026/7u10_26273.map" } resolution = 3.0 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= 0.002 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 21 5.16 5 C 2178 2.51 5 N 531 2.21 5 O 699 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 3429 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1087 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Restraints were copied for chains: B, C Time building chain proxies: 0.90, per 1000 atoms: 0.26 Number of scatterers: 3429 At special positions: 0 Unit cell: (105.252, 98.808, 32.22, 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 21 16.00 O 699 8.00 N 531 7.00 C 2178 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 253 " 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 Links applied NAG-ASN " NAG A 301 " - " ASN A 183 " " NAG A 302 " - " ASN A 151 " " NAG A 303 " - " ASN A 145 " " NAG A 304 " - " ASN A 164 " " NAG B 301 " - " ASN B 183 " " NAG B 302 " - " ASN B 151 " " NAG B 303 " - " ASN B 145 " " NAG B 304 " - " ASN B 164 " " NAG C 301 " - " ASN C 183 " " NAG C 302 " - " ASN C 151 " " NAG C 303 " - " ASN C 145 " " NAG C 304 " - " ASN C 164 " Time building additional restraints: 0.25 Conformation dependent library (CDL) restraints added in 120.4 milliseconds 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 63.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 126 removed outlier: 6.501A pdb=" N VAL A 123 " --> pdb=" O LYS B 124 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE B 126 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR A 125 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL B 123 " --> pdb=" O LYS C 124 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE C 126 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N TYR B 125 " --> pdb=" O ILE C 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 137 removed outlier: 6.396A pdb=" N LYS A 129 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N TYR B 132 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N ALA A 131 " --> pdb=" O TYR B 132 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N SER B 134 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N VAL A 133 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 9.618A pdb=" N ASP B 136 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N TYR A 135 " --> pdb=" O ASP B 136 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS B 129 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N TYR C 132 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N ALA B 131 " --> pdb=" O TYR C 132 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N SER C 134 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N VAL B 133 " --> pdb=" O SER C 134 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N ASP C 136 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N TYR B 135 " --> pdb=" O ASP C 136 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 160 removed outlier: 6.993A pdb=" N ILE A 146 " --> pdb=" O ASN B 145 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N THR B 147 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ASN A 148 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N THR B 149 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU A 150 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ASN B 151 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE A 152 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N THR B 153 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASN A 154 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASN B 155 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASN A 156 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N TYR B 157 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TYR A 158 " --> pdb=" O TYR B 157 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N SER B 159 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL A 160 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE B 146 " --> pdb=" O ASN C 145 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR C 147 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ASN B 148 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR C 149 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU B 150 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ASN C 151 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE B 152 " --> pdb=" O ASN C 151 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR C 153 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASN B 154 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASN C 155 " --> pdb=" O ASN B 154 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ASN B 156 " --> pdb=" O ASN C 155 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TYR C 157 " --> pdb=" O ASN B 156 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR B 158 " --> pdb=" O TYR C 157 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N SER C 159 " --> pdb=" O TYR B 158 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL B 160 " --> pdb=" O SER C 159 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 163 through 165 removed outlier: 6.047A pdb=" N ASN B 164 " --> pdb=" O ILE C 165 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 168 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 180 through 181 removed outlier: 6.633A pdb=" N ARG A 180 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG B 180 " --> pdb=" O LEU C 181 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 185 through 187 removed outlier: 6.503A pdb=" N THR A 185 " --> pdb=" O ILE B 186 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 191 through 198 removed outlier: 8.916A pdb=" N MET A 192 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N ILE B 195 " --> pdb=" O MET A 192 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLN A 194 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N TYR B 197 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP A 196 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N MET B 192 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N ILE C 195 " --> pdb=" O MET B 192 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLN B 194 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N TYR C 197 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP B 196 " --> pdb=" O TYR C 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 201 through 204 removed outlier: 6.382A pdb=" N VAL A 202 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL B 202 " --> pdb=" O ILE C 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 209 through 228 removed outlier: 6.131A pdb=" N TYR A 209 " --> pdb=" O MET B 210 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASP B 212 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TYR A 211 " --> pdb=" O ASP B 212 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N CYS B 214 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N PHE A 213 " --> pdb=" O CYS B 214 " (cutoff:3.500A) removed outlier: 10.563A pdb=" N LEU B 216 " --> pdb=" O PHE A 213 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N THR A 215 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 9.979A pdb=" N SER B 218 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N ILE A 217 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 10.126A pdb=" N LYS B 220 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE A 219 " --> pdb=" O LYS B 220 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N HIS B 222 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL A 221 " --> pdb=" O HIS B 222 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE B 224 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ASN A 223 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N LEU B 226 " --> pdb=" O ASN A 223 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N VAL A 225 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 10.386A pdb=" N MET B 228 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 9.560A pdb=" N MET A 227 " --> pdb=" O MET B 228 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N TYR B 209 " --> pdb=" O MET C 210 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ASP C 212 " --> pdb=" O TYR B 209 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N TYR B 211 " --> pdb=" O ASP C 212 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N CYS C 214 " --> pdb=" O TYR B 211 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N PHE B 213 " --> pdb=" O CYS C 214 " (cutoff:3.500A) removed outlier: 10.587A pdb=" N LEU C 216 " --> pdb=" O PHE B 213 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N THR B 215 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N SER C 218 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N ILE B 217 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 10.142A pdb=" N LYS C 220 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ILE B 219 " --> pdb=" O LYS C 220 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N HIS C 222 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL B 221 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ILE C 224 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ASN B 223 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 10.221A pdb=" N LEU C 226 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N VAL B 225 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 10.369A pdb=" N MET C 228 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N MET B 227 " --> pdb=" O MET C 228 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 233 through 243 Processing sheet with id=AB3, first strand: chain 'A' and resid 246 through 249 54 hydrogen bonds defined for protein. 162 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: 0.45 Time building geometry restraints manager: 0.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1053 1.34 - 1.46: 816 1.46 - 1.58: 1578 1.58 - 1.70: 0 1.70 - 1.82: 36 Bond restraints: 3483 Sorted by residual: bond pdb=" C1 NAG C 304 " pdb=" O5 NAG C 304 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C1 NAG B 304 " pdb=" O5 NAG B 304 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C1 NAG A 304 " pdb=" O5 NAG A 304 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C1 NAG C 303 " pdb=" O5 NAG C 303 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.26e+00 bond pdb=" C1 NAG B 303 " pdb=" O5 NAG B 303 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.17e+00 ... (remaining 3478 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.88: 4162 0.88 - 1.76: 434 1.76 - 2.64: 111 2.64 - 3.52: 21 3.52 - 4.40: 9 Bond angle restraints: 4737 Sorted by residual: angle pdb=" CG1 VAL C 230 " pdb=" CB VAL C 230 " pdb=" CG2 VAL C 230 " ideal model delta sigma weight residual 110.80 106.40 4.40 2.20e+00 2.07e-01 4.00e+00 angle pdb=" CG1 VAL B 230 " pdb=" CB VAL B 230 " pdb=" CG2 VAL B 230 " ideal model delta sigma weight residual 110.80 106.45 4.35 2.20e+00 2.07e-01 3.91e+00 angle pdb=" CG1 VAL A 230 " pdb=" CB VAL A 230 " pdb=" CG2 VAL A 230 " ideal model delta sigma weight residual 110.80 106.47 4.33 2.20e+00 2.07e-01 3.87e+00 angle pdb=" CA GLN C 245 " pdb=" CB GLN C 245 " pdb=" CG GLN C 245 " ideal model delta sigma weight residual 114.10 117.79 -3.69 2.00e+00 2.50e-01 3.41e+00 angle pdb=" CA GLN A 245 " pdb=" CB GLN A 245 " pdb=" CG GLN A 245 " ideal model delta sigma weight residual 114.10 117.77 -3.67 2.00e+00 2.50e-01 3.36e+00 ... (remaining 4732 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.27: 1740 13.27 - 26.53: 156 26.53 - 39.80: 64 39.80 - 53.06: 26 53.06 - 66.33: 12 Dihedral angle restraints: 1998 sinusoidal: 780 harmonic: 1218 Sorted by residual: dihedral pdb=" CB CYS C 214 " pdb=" SG CYS C 214 " pdb=" SG CYS C 253 " pdb=" CB CYS C 253 " ideal model delta sinusoidal sigma weight residual -86.00 -31.95 -54.05 1 1.00e+01 1.00e-02 3.96e+01 dihedral pdb=" CB CYS A 214 " pdb=" SG CYS A 214 " pdb=" SG CYS A 253 " pdb=" CB CYS A 253 " ideal model delta sinusoidal sigma weight residual -86.00 -32.05 -53.95 1 1.00e+01 1.00e-02 3.95e+01 dihedral pdb=" CB CYS B 214 " pdb=" SG CYS B 214 " pdb=" SG CYS B 253 " pdb=" CB CYS B 253 " ideal model delta sinusoidal sigma weight residual -86.00 -32.07 -53.93 1 1.00e+01 1.00e-02 3.95e+01 ... (remaining 1995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 354 0.036 - 0.072: 147 0.072 - 0.108: 58 0.108 - 0.144: 38 0.144 - 0.180: 6 Chirality restraints: 603 Sorted by residual: chirality pdb=" C1 NAG C 301 " pdb=" ND2 ASN C 183 " pdb=" C2 NAG C 301 " pdb=" O5 NAG C 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.14e-01 chirality pdb=" C1 NAG A 301 " pdb=" ND2 ASN A 183 " pdb=" C2 NAG A 301 " pdb=" O5 NAG A 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.94e-01 chirality pdb=" C1 NAG B 301 " pdb=" ND2 ASN B 183 " pdb=" C2 NAG B 301 " pdb=" O5 NAG B 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.81e-01 ... (remaining 600 not shown) Planarity restraints: 585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 158 " 0.003 2.00e-02 2.50e+03 1.31e-02 3.43e+00 pdb=" CG TYR A 158 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR A 158 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR A 158 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A 158 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 158 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 158 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 158 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 158 " 0.003 2.00e-02 2.50e+03 1.29e-02 3.32e+00 pdb=" CG TYR B 158 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR B 158 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR B 158 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 158 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B 158 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 158 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 158 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 158 " 0.003 2.00e-02 2.50e+03 1.28e-02 3.27e+00 pdb=" CG TYR C 158 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR C 158 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR C 158 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR C 158 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR C 158 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 158 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 158 " -0.001 2.00e-02 2.50e+03 ... (remaining 582 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 286 2.76 - 3.30: 3209 3.30 - 3.83: 5871 3.83 - 4.37: 6193 4.37 - 4.90: 12302 Nonbonded interactions: 27861 Sorted by model distance: nonbonded pdb=" OE1 GLN C 229 " pdb=" OG1 THR C 234 " model vdw 2.230 3.040 nonbonded pdb=" OE1 GLN B 229 " pdb=" OG1 THR B 234 " model vdw 2.230 3.040 nonbonded pdb=" OE1 GLN A 229 " pdb=" OG1 THR A 234 " model vdw 2.230 3.040 nonbonded pdb=" N SER B 120 " pdb=" OE1 GLU C 241 " model vdw 2.261 3.120 nonbonded pdb=" NZ LYS B 129 " pdb=" OD2 ASP B 136 " model vdw 2.271 3.120 ... (remaining 27856 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 4.190 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: 0.020 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.040 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 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 0.071 3498 Z= 0.216 Angle : 0.703 6.533 4779 Z= 0.345 Chirality : 0.053 0.180 603 Planarity : 0.002 0.013 573 Dihedral : 14.036 66.328 1209 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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: -2.82 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 247 TYR 0.027 0.002 TYR A 158 PHE 0.013 0.002 PHE A 213 HIS 0.002 0.001 HIS C 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.22 ( 3483) covalent geometry : angle 0.63816 / 0.33 ( 4737) SS BOND : bond 0.00043 / 0.02 ( 3) SS BOND : angle 2.89744 / 1.56 ( 6) hydrogen bonds : bond 0.15669 / 11.13 ( 54) hydrogen bonds : angle 8.70705 / 6.37 ( 162) link_NAG-ASN : bond 0.00488 / 0.33 ( 12) link_NAG-ASN : angle 3.26437 / 2.23 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: B 234 THR cc_start: 0.7622 (t) cc_final: 0.7412 (t) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2833 time to fit residues: 22.9928 Evaluate side-chains 49 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN A 168 GLN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5162 r_free = 0.5162 target = 0.175934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.4958 r_free = 0.4958 target = 0.155055 restraints weight = 5590.564| |-----------------------------------------------------------------------------| r_work (start): 0.5049 rms_B_bonded: 4.13 r_work: 0.4921 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.4921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 3498 Z= 0.308 Angle : 0.969 12.144 4779 Z= 0.479 Chirality : 0.067 0.510 603 Planarity : 0.005 0.041 573 Dihedral : 7.969 54.627 450 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.76 % Allowed : 15.34 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.35 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 247 TYR 0.024 0.004 TYR B 157 PHE 0.017 0.004 PHE C 237 HIS 0.004 0.001 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00701 / 0.31 ( 3483) covalent geometry : angle 0.84910 / 0.45 ( 4737) SS BOND : bond 0.01164 / 0.59 ( 3) SS BOND : angle 2.32075 / 1.28 ( 6) hydrogen bonds : bond 0.03584 / 2.80 ( 54) hydrogen bonds : angle 5.79881 / 4.19 ( 162) link_NAG-ASN : bond 0.00595 / 0.39 ( 12) link_NAG-ASN : angle 5.36819 / 4.17 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 SER cc_start: 0.7704 (t) cc_final: 0.7342 (t) REVERT: A 135 TYR cc_start: 0.7507 (OUTLIER) cc_final: 0.7300 (m-10) REVERT: A 138 GLN cc_start: 0.6946 (tp40) cc_final: 0.5784 (mm-40) REVERT: B 135 TYR cc_start: 0.6935 (OUTLIER) cc_final: 0.5931 (m-10) REVERT: C 135 TYR cc_start: 0.6851 (OUTLIER) cc_final: 0.5955 (m-10) REVERT: C 183 ASN cc_start: 0.7098 (m110) cc_final: 0.5865 (p0) REVERT: C 227 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7918 (mmt) outliers start: 18 outliers final: 7 residues processed: 62 average time/residue: 0.3940 time to fit residues: 25.3955 Evaluate side-chains 51 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 GLN B 168 GLN B 170 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5357 r_free = 0.5357 target = 0.184795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.5184 r_free = 0.5184 target = 0.165900 restraints weight = 4354.840| |-----------------------------------------------------------------------------| r_work (start): 0.5256 rms_B_bonded: 3.47 r_work: 0.5155 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.5155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3498 Z= 0.193 Angle : 0.751 9.627 4779 Z= 0.373 Chirality : 0.060 0.402 603 Planarity : 0.003 0.013 573 Dihedral : 7.409 54.845 450 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 5.56 % Allowed : 19.84 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.35 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 140 TYR 0.015 0.003 TYR C 125 PHE 0.009 0.002 PHE C 171 HIS 0.003 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 ( 3483) covalent geometry : angle 0.66199 / 0.35 ( 4737) SS BOND : bond 0.00441 / 0.21 ( 3) SS BOND : angle 1.49667 / 0.82 ( 6) hydrogen bonds : bond 0.02940 / 2.25 ( 54) hydrogen bonds : angle 5.46357 / 3.93 ( 162) link_NAG-ASN : bond 0.00417 / 0.27 ( 12) link_NAG-ASN : angle 4.09229 / 3.16 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 38 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 GLU cc_start: 0.6887 (mm-30) cc_final: 0.6491 (mp0) REVERT: A 228 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7337 (tmm) REVERT: C 227 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7847 (mmt) REVERT: C 234 THR cc_start: 0.8738 (t) cc_final: 0.8409 (m) outliers start: 21 outliers final: 10 residues processed: 53 average time/residue: 0.3195 time to fit residues: 17.8337 Evaluate side-chains 44 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 16 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5375 r_free = 0.5375 target = 0.190001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5195 r_free = 0.5195 target = 0.170542 restraints weight = 4351.194| |-----------------------------------------------------------------------------| r_work (start): 0.5197 rms_B_bonded: 3.50 r_work: 0.5084 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.5084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3498 Z= 0.153 Angle : 0.692 8.670 4779 Z= 0.346 Chirality : 0.059 0.371 603 Planarity : 0.002 0.010 573 Dihedral : 7.145 54.543 450 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.50 % Allowed : 22.49 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.39 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 140 TYR 0.022 0.002 TYR A 143 PHE 0.006 0.001 PHE C 171 HIS 0.004 0.001 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 3483) covalent geometry : angle 0.62030 / 0.33 ( 4737) SS BOND : bond 0.00112 / 0.05 ( 3) SS BOND : angle 1.46409 / 0.74 ( 6) hydrogen bonds : bond 0.02675 / 2.03 ( 54) hydrogen bonds : angle 5.30058 / 3.80 ( 162) link_NAG-ASN : bond 0.00395 / 0.26 ( 12) link_NAG-ASN : angle 3.53672 / 2.72 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 35 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 THR cc_start: 0.7600 (OUTLIER) cc_final: 0.7217 (p) REVERT: C 135 TYR cc_start: 0.7453 (OUTLIER) cc_final: 0.7098 (m-10) REVERT: C 227 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7906 (mmt) REVERT: C 234 THR cc_start: 0.8750 (t) cc_final: 0.8414 (m) outliers start: 17 outliers final: 10 residues processed: 48 average time/residue: 0.3337 time to fit residues: 16.8562 Evaluate side-chains 45 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 32 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 245 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 242 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 = 0.5346 r_free = 0.5346 target = 0.184079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5173 r_free = 0.5173 target = 0.165332 restraints weight = 4355.330| |-----------------------------------------------------------------------------| r_work (start): 0.5184 rms_B_bonded: 3.43 r_work: 0.5071 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.5071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3498 Z= 0.157 Angle : 0.690 8.518 4779 Z= 0.347 Chirality : 0.059 0.371 603 Planarity : 0.002 0.013 573 Dihedral : 7.038 54.207 450 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 5.56 % Allowed : 22.22 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.38 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 247 TYR 0.017 0.002 TYR A 143 PHE 0.007 0.001 PHE B 237 HIS 0.004 0.001 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 3483) covalent geometry : angle 0.62225 / 0.33 ( 4737) SS BOND : bond 0.00107 / 0.05 ( 3) SS BOND : angle 1.33002 / 0.64 ( 6) hydrogen bonds : bond 0.02436 / 1.85 ( 54) hydrogen bonds : angle 5.16723 / 3.68 ( 162) link_NAG-ASN : bond 0.00375 / 0.24 ( 12) link_NAG-ASN : angle 3.45121 / 2.64 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 30 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 TYR cc_start: 0.7780 (OUTLIER) cc_final: 0.7487 (m-10) REVERT: A 184 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7847 (mp) REVERT: A 185 THR cc_start: 0.7665 (OUTLIER) cc_final: 0.7315 (p) REVERT: B 234 THR cc_start: 0.7938 (OUTLIER) cc_final: 0.7737 (m) REVERT: C 135 TYR cc_start: 0.7360 (OUTLIER) cc_final: 0.7020 (m-10) REVERT: C 227 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7869 (mmt) REVERT: C 234 THR cc_start: 0.8762 (t) cc_final: 0.8504 (m) outliers start: 21 outliers final: 12 residues processed: 47 average time/residue: 0.2858 time to fit residues: 14.2547 Evaluate side-chains 48 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 30 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 245 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 27 optimal weight: 0.3980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 242 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 = 0.5468 r_free = 0.5468 target = 0.193342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5292 r_free = 0.5292 target = 0.173256 restraints weight = 4788.591| |-----------------------------------------------------------------------------| r_work (start): 0.5337 rms_B_bonded: 3.32 r_work: 0.5254 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.5254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3498 Z= 0.133 Angle : 0.655 7.757 4779 Z= 0.328 Chirality : 0.058 0.343 603 Planarity : 0.002 0.013 573 Dihedral : 6.768 53.407 450 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.97 % Allowed : 23.28 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.35 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 140 TYR 0.015 0.002 TYR A 143 PHE 0.007 0.001 PHE B 237 HIS 0.004 0.001 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 3483) covalent geometry : angle 0.59418 / 0.32 ( 4737) SS BOND : bond 0.00255 / 0.13 ( 3) SS BOND : angle 1.12381 / 0.56 ( 6) hydrogen bonds : bond 0.02257 / 1.71 ( 54) hydrogen bonds : angle 5.06558 / 3.59 ( 162) link_NAG-ASN : bond 0.00389 / 0.25 ( 12) link_NAG-ASN : angle 3.20069 / 2.42 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 GLN cc_start: 0.2697 (OUTLIER) cc_final: 0.2299 (pp30) REVERT: A 185 THR cc_start: 0.7093 (OUTLIER) cc_final: 0.6828 (p) REVERT: B 210 MET cc_start: 0.6073 (mtp) cc_final: 0.5563 (mtt) REVERT: C 213 PHE cc_start: 0.6443 (m-10) cc_final: 0.5567 (p90) REVERT: C 227 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7626 (mmt) REVERT: C 234 THR cc_start: 0.8627 (t) cc_final: 0.8331 (m) outliers start: 15 outliers final: 9 residues processed: 50 average time/residue: 0.3180 time to fit residues: 16.6841 Evaluate side-chains 44 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 245 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 GLN A 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5875 r_free = 0.5875 target = 0.453686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.6761 r_free = 0.6761 target = 0.375752 restraints weight = 5400.240| |-----------------------------------------------------------------------------| r_work (start): 0.5164 rms_B_bonded: 1.10 r_work: 0.5063 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.5000 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.5000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3498 Z= 0.160 Angle : 0.716 9.079 4779 Z= 0.354 Chirality : 0.059 0.387 603 Planarity : 0.003 0.028 573 Dihedral : 6.794 52.688 450 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 5.03 % Allowed : 21.96 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.39 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 140 TYR 0.016 0.002 TYR A 143 PHE 0.007 0.001 PHE C 171 HIS 0.004 0.001 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 3483) covalent geometry : angle 0.64517 / 0.34 ( 4737) SS BOND : bond 0.00160 / 0.08 ( 3) SS BOND : angle 1.23248 / 0.58 ( 6) hydrogen bonds : bond 0.02385 / 1.82 ( 54) hydrogen bonds : angle 5.12949 / 3.67 ( 162) link_NAG-ASN : bond 0.00376 / 0.24 ( 12) link_NAG-ASN : angle 3.61378 / 2.76 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 34 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 THR cc_start: 0.7995 (OUTLIER) cc_final: 0.7661 (p) REVERT: B 210 MET cc_start: 0.7021 (mtp) cc_final: 0.6326 (mtt) REVERT: C 183 ASN cc_start: 0.6064 (m110) cc_final: 0.5303 (p0) REVERT: C 213 PHE cc_start: 0.7067 (m-10) cc_final: 0.5921 (p90) REVERT: C 227 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7844 (mmt) REVERT: C 234 THR cc_start: 0.8765 (t) cc_final: 0.8477 (m) outliers start: 19 outliers final: 10 residues processed: 50 average time/residue: 0.2987 time to fit residues: 15.7498 Evaluate side-chains 43 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 5 optimal weight: 0.9990 chunk 34 optimal weight: 0.0170 chunk 11 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN A 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5521 r_free = 0.5521 target = 0.198366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5344 r_free = 0.5344 target = 0.177638 restraints weight = 4766.904| |-----------------------------------------------------------------------------| r_work (start): 0.5252 rms_B_bonded: 3.38 r_work: 0.5134 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.5134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3498 Z= 0.111 Angle : 0.658 6.953 4779 Z= 0.323 Chirality : 0.057 0.317 603 Planarity : 0.002 0.025 573 Dihedral : 6.233 50.131 450 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.17 % Allowed : 24.07 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.29 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 140 TYR 0.013 0.001 TYR A 143 PHE 0.013 0.001 PHE C 237 HIS 0.003 0.001 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 3483) covalent geometry : angle 0.59722 / 0.31 ( 4737) SS BOND : bond 0.00125 / 0.06 ( 3) SS BOND : angle 0.77372 / 0.39 ( 6) hydrogen bonds : bond 0.02449 / 1.83 ( 54) hydrogen bonds : angle 5.18096 / 3.74 ( 162) link_NAG-ASN : bond 0.00452 / 0.30 ( 12) link_NAG-ASN : angle 3.23243 / 2.48 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 THR cc_start: 0.8116 (OUTLIER) cc_final: 0.7829 (p) REVERT: B 210 MET cc_start: 0.6830 (mtp) cc_final: 0.6237 (mtt) REVERT: C 213 PHE cc_start: 0.6999 (m-10) cc_final: 0.5891 (p90) REVERT: C 234 THR cc_start: 0.8753 (t) cc_final: 0.8469 (m) outliers start: 12 outliers final: 7 residues processed: 46 average time/residue: 0.2788 time to fit residues: 13.4879 Evaluate side-chains 42 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 245 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 6 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 229 GLN B 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5072 r_free = 0.5072 target = 0.155882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.135608 restraints weight = 5067.176| |-----------------------------------------------------------------------------| r_work (start): 0.5044 rms_B_bonded: 3.86 r_work: 0.4948 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6039 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3498 Z= 0.198 Angle : 0.770 9.385 4779 Z= 0.381 Chirality : 0.061 0.405 603 Planarity : 0.003 0.031 573 Dihedral : 6.698 50.771 450 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.17 % Allowed : 24.60 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.48 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 140 TYR 0.018 0.003 TYR C 143 PHE 0.009 0.002 PHE C 171 HIS 0.004 0.001 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 ( 3483) covalent geometry : angle 0.68805 / 0.36 ( 4737) SS BOND : bond 0.00167 / 0.09 ( 3) SS BOND : angle 1.42232 / 0.64 ( 6) hydrogen bonds : bond 0.02469 / 1.87 ( 54) hydrogen bonds : angle 5.26806 / 3.80 ( 162) link_NAG-ASN : bond 0.00477 / 0.29 ( 12) link_NAG-ASN : angle 4.01331 / 2.99 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 TYR cc_start: 0.7820 (OUTLIER) cc_final: 0.7464 (m-80) REVERT: A 185 THR cc_start: 0.7209 (OUTLIER) cc_final: 0.6895 (p) REVERT: B 210 MET cc_start: 0.6055 (mtp) cc_final: 0.5445 (mtt) REVERT: C 183 ASN cc_start: 0.6612 (m110) cc_final: 0.5843 (p0) REVERT: C 213 PHE cc_start: 0.6303 (m-10) cc_final: 0.5508 (p90) REVERT: C 234 THR cc_start: 0.8609 (t) cc_final: 0.8284 (m) outliers start: 12 outliers final: 6 residues processed: 44 average time/residue: 0.3269 time to fit residues: 15.0256 Evaluate side-chains 40 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 229 GLN B 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5414 r_free = 0.5414 target = 0.183354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5230 r_free = 0.5230 target = 0.163289 restraints weight = 4820.233| |-----------------------------------------------------------------------------| r_work (start): 0.5224 rms_B_bonded: 3.46 r_work: 0.5114 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.5114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3498 Z= 0.119 Angle : 0.686 8.975 4779 Z= 0.336 Chirality : 0.058 0.331 603 Planarity : 0.002 0.029 573 Dihedral : 6.220 50.549 450 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.17 % Allowed : 25.13 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.38 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 247 TYR 0.012 0.001 TYR A 143 PHE 0.005 0.001 PHE B 171 HIS 0.004 0.001 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 3483) covalent geometry : angle 0.61789 / 0.32 ( 4737) SS BOND : bond 0.00128 / 0.07 ( 3) SS BOND : angle 0.78526 / 0.40 ( 6) hydrogen bonds : bond 0.02363 / 1.78 ( 54) hydrogen bonds : angle 5.15927 / 3.74 ( 162) link_NAG-ASN : bond 0.00485 / 0.29 ( 12) link_NAG-ASN : angle 3.49227 / 2.56 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 GLN cc_start: 0.3763 (OUTLIER) cc_final: 0.3338 (pp30) REVERT: A 185 THR cc_start: 0.8038 (OUTLIER) cc_final: 0.7738 (p) REVERT: B 210 MET cc_start: 0.6990 (mtp) cc_final: 0.6254 (mtt) REVERT: C 213 PHE cc_start: 0.6960 (m-10) cc_final: 0.5899 (p90) REVERT: C 234 THR cc_start: 0.8803 (t) cc_final: 0.8506 (m) outliers start: 12 outliers final: 7 residues processed: 48 average time/residue: 0.2956 time to fit residues: 14.9115 Evaluate side-chains 45 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 10 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 GLN A 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5094 r_free = 0.5094 target = 0.161217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4919 r_free = 0.4919 target = 0.140505 restraints weight = 5232.191| |-----------------------------------------------------------------------------| r_work (start): 0.5080 rms_B_bonded: 3.81 r_work: 0.4955 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.4955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 0.5421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 3498 Z= 0.210 Angle : 0.794 9.934 4779 Z= 0.391 Chirality : 0.062 0.427 603 Planarity : 0.003 0.033 573 Dihedral : 6.861 51.295 450 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 3.70 % Allowed : 24.87 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.53 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 140 TYR 0.018 0.003 TYR C 143 PHE 0.008 0.002 PHE C 171 HIS 0.003 0.001 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 ( 3483) covalent geometry : angle 0.70886 / 0.37 ( 4737) SS BOND : bond 0.00235 / 0.12 ( 3) SS BOND : angle 1.55943 / 0.72 ( 6) hydrogen bonds : bond 0.02483 / 1.90 ( 54) hydrogen bonds : angle 5.21544 / 3.77 ( 162) link_NAG-ASN : bond 0.00515 / 0.31 ( 12) link_NAG-ASN : angle 4.14738 / 3.10 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1204.08 seconds wall clock time: 21 minutes 20.96 seconds (1280.96 seconds total)