Starting phenix.real_space_refine on Tue Mar 3 11:47:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u10_26273/03_2026/7u10_26273.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u10_26273/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7u10_26273/03_2026/7u10_26273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u10_26273/03_2026/7u10_26273.map" model { file = "/net/cci-nas-00/data/ceres_data/7u10_26273/03_2026/7u10_26273.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u10_26273/03_2026/7u10_26273.cif" } 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-5986/lib/python3.9/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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Restraints were copied for chains: B, C Time building chain proxies: 0.88, 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: 0.31 Conformation dependent library (CDL) restraints added in 129.2 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: 0.48 Time building geometry restraints manager: 0.43 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 - 24.75: 2088 24.75 - 49.51: 126 49.51 - 74.26: 21 74.26 - 99.01: 12 99.01 - 123.76: 3 Dihedral angle restraints: 2250 sinusoidal: 1032 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 2247 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: 3.580 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: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.700 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 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 : 17.217 123.763 1461 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 covalent geometry : bond 0.00433 ( 3483) covalent geometry : angle 0.63816 ( 4737) SS BOND : bond 0.00043 ( 3) SS BOND : angle 2.89744 ( 6) hydrogen bonds : bond 0.15669 ( 54) hydrogen bonds : angle 8.70705 ( 162) link_NAG-ASN : bond 0.00488 ( 12) link_NAG-ASN : angle 3.26437 ( 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 : 0.083 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: 0.2922 time to fit residues: 23.7049 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... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 168 GLN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5168 r_free = 0.5168 target = 0.175999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4961 r_free = 0.4961 target = 0.154959 restraints weight = 5583.170| |-----------------------------------------------------------------------------| r_work (start): 0.5057 rms_B_bonded: 4.10 r_work: 0.4931 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.4931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 3498 Z= 0.310 Angle : 0.967 12.431 4779 Z= 0.475 Chirality : 0.065 0.510 603 Planarity : 0.005 0.037 573 Dihedral : 16.997 118.128 702 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 5.03 % Allowed : 15.61 % Favored : 79.37 % 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: -3.30 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (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 158 PHE 0.018 0.004 PHE C 237 HIS 0.004 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00704 ( 3483) covalent geometry : angle 0.83667 ( 4737) SS BOND : bond 0.00449 ( 3) SS BOND : angle 2.18171 ( 6) hydrogen bonds : bond 0.03706 ( 54) hydrogen bonds : angle 5.81777 ( 162) link_NAG-ASN : bond 0.00564 ( 12) link_NAG-ASN : angle 5.57807 ( 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: 19 poor density : 48 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 SER cc_start: 0.7673 (t) cc_final: 0.7293 (t) REVERT: A 158 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.7643 (m-80) REVERT: B 135 TYR cc_start: 0.6921 (OUTLIER) cc_final: 0.5970 (m-10) REVERT: B 182 ASN cc_start: 0.6179 (t0) cc_final: 0.5969 (t0) REVERT: C 135 TYR cc_start: 0.6921 (OUTLIER) cc_final: 0.5895 (m-10) REVERT: C 227 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7919 (mmt) outliers start: 19 outliers final: 8 residues processed: 62 average time/residue: 0.4226 time to fit residues: 27.2122 Evaluate side-chains 51 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 TYR 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 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: 3.9990 chunk 5 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.5337 r_free = 0.5337 target = 0.182084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.5158 r_free = 0.5158 target = 0.163270 restraints weight = 4378.828| |-----------------------------------------------------------------------------| r_work (start): 0.5241 rms_B_bonded: 3.48 r_work: 0.5147 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.5147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3498 Z= 0.208 Angle : 0.797 10.473 4779 Z= 0.391 Chirality : 0.060 0.433 603 Planarity : 0.003 0.015 573 Dihedral : 16.568 117.549 702 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 5.56 % Allowed : 19.05 % Favored : 75.40 % 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: -3.37 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 140 TYR 0.016 0.003 TYR A 157 PHE 0.009 0.002 PHE C 171 HIS 0.003 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 3483) covalent geometry : angle 0.69537 ( 4737) SS BOND : bond 0.00252 ( 3) SS BOND : angle 1.81130 ( 6) hydrogen bonds : bond 0.03011 ( 54) hydrogen bonds : angle 5.48615 ( 162) link_NAG-ASN : bond 0.00412 ( 12) link_NAG-ASN : angle 4.49577 ( 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 61 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 40 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 TYR cc_start: 0.7756 (OUTLIER) cc_final: 0.7203 (m-10) REVERT: A 161 GLU cc_start: 0.6958 (mm-30) cc_final: 0.6570 (mp0) REVERT: C 183 ASN cc_start: 0.7034 (m110) cc_final: 0.5923 (p0) REVERT: C 227 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7808 (mmt) REVERT: C 234 THR cc_start: 0.8746 (t) cc_final: 0.8412 (m) outliers start: 21 outliers final: 10 residues processed: 55 average time/residue: 0.3146 time to fit residues: 18.1154 Evaluate side-chains 46 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.077 ------------------------------------------------------------------------------- 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 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 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: 10.0000 chunk 9 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 229 GLN B 154 ASN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5913 r_free = 0.5913 target = 0.461336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.6796 r_free = 0.6796 target = 0.386240 restraints weight = 5256.033| |-----------------------------------------------------------------------------| r_work (start): 0.5430 rms_B_bonded: 1.14 r_work: 0.5548 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.5501 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work (final): 0.5501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3498 Z= 0.121 Angle : 0.688 8.262 4779 Z= 0.334 Chirality : 0.057 0.360 603 Planarity : 0.002 0.008 573 Dihedral : 15.676 113.700 702 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.50 % Allowed : 21.16 % Favored : 74.34 % 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: -3.30 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 140 TYR 0.020 0.002 TYR A 143 PHE 0.004 0.001 PHE B 237 HIS 0.004 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 3483) covalent geometry : angle 0.61585 ( 4737) SS BOND : bond 0.00111 ( 3) SS BOND : angle 1.02642 ( 6) hydrogen bonds : bond 0.02609 ( 54) hydrogen bonds : angle 5.26255 ( 162) link_NAG-ASN : bond 0.00391 ( 12) link_NAG-ASN : angle 3.58150 ( 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 55 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 38 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 THR cc_start: 0.8193 (OUTLIER) cc_final: 0.7879 (p) REVERT: C 227 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7863 (mmt) outliers start: 17 outliers final: 6 residues processed: 50 average time/residue: 0.3062 time to fit residues: 16.1047 Evaluate side-chains 36 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 231 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: 0.8980 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN ** B 242 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 = 0.5292 r_free = 0.5292 target = 0.178211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.5106 r_free = 0.5106 target = 0.159635 restraints weight = 4468.382| |-----------------------------------------------------------------------------| r_work (start): 0.5306 rms_B_bonded: 3.46 r_work: 0.5183 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.5183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5330 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3498 Z= 0.206 Angle : 0.788 10.149 4779 Z= 0.388 Chirality : 0.061 0.429 603 Planarity : 0.003 0.021 573 Dihedral : 16.118 116.574 702 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 6.08 % Allowed : 20.37 % Favored : 73.54 % 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: -3.45 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 140 TYR 0.018 0.003 TYR A 143 PHE 0.010 0.002 PHE C 171 HIS 0.003 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 3483) covalent geometry : angle 0.70322 ( 4737) SS BOND : bond 0.00143 ( 3) SS BOND : angle 1.75382 ( 6) hydrogen bonds : bond 0.02633 ( 54) hydrogen bonds : angle 5.19497 ( 162) link_NAG-ASN : bond 0.00412 ( 12) link_NAG-ASN : angle 4.09961 ( 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 56 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 33 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 TYR cc_start: 0.7734 (OUTLIER) cc_final: 0.7387 (m-80) REVERT: C 183 ASN cc_start: 0.6683 (m110) cc_final: 0.6123 (p0) REVERT: C 227 MET cc_start: 0.6892 (OUTLIER) cc_final: 0.6660 (mmt) REVERT: C 228 MET cc_start: 0.8114 (tpt) cc_final: 0.7406 (tpt) outliers start: 23 outliers final: 10 residues processed: 50 average time/residue: 0.2995 time to fit residues: 15.7619 Evaluate side-chains 42 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 30 time to evaluate : 0.143 ------------------------------------------------------------------------------- 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 185 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 234 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN ** B 242 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 = 0.5407 r_free = 0.5407 target = 0.251238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5282 r_free = 0.5282 target = 0.227707 restraints weight = 5718.693| |-----------------------------------------------------------------------------| r_work (start): 0.5278 rms_B_bonded: 4.27 r_work: 0.5140 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.5140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3498 Z= 0.132 Angle : 0.711 8.980 4779 Z= 0.343 Chirality : 0.058 0.389 603 Planarity : 0.002 0.010 573 Dihedral : 15.337 113.202 702 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.44 % Allowed : 23.81 % 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: -3.38 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 180 TYR 0.014 0.002 TYR A 143 PHE 0.005 0.001 PHE B 171 HIS 0.004 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 3483) covalent geometry : angle 0.64065 ( 4737) SS BOND : bond 0.00123 ( 3) SS BOND : angle 1.15086 ( 6) hydrogen bonds : bond 0.02338 ( 54) hydrogen bonds : angle 5.04993 ( 162) link_NAG-ASN : bond 0.00386 ( 12) link_NAG-ASN : angle 3.57973 ( 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 42 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 29 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 THR cc_start: 0.7807 (OUTLIER) cc_final: 0.7458 (p) REVERT: C 227 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7913 (mmt) outliers start: 13 outliers final: 7 residues processed: 39 average time/residue: 0.3726 time to fit residues: 15.2142 Evaluate side-chains 37 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 215 THR 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: 1.9990 chunk 15 optimal weight: 4.9990 chunk 36 optimal weight: 0.0980 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 26 optimal weight: 0.1980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN ** B 242 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 = 0.5488 r_free = 0.5488 target = 0.188984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5291 r_free = 0.5291 target = 0.167552 restraints weight = 4815.040| |-----------------------------------------------------------------------------| r_work (start): 0.5270 rms_B_bonded: 3.58 r_work: 0.5153 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.5153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3498 Z= 0.107 Angle : 0.669 9.597 4779 Z= 0.322 Chirality : 0.056 0.318 603 Planarity : 0.002 0.011 573 Dihedral : 14.589 109.479 702 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.91 % Allowed : 23.81 % Favored : 73.28 % 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: -3.26 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 140 TYR 0.012 0.001 TYR A 143 PHE 0.004 0.001 PHE B 171 HIS 0.003 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 3483) covalent geometry : angle 0.61382 ( 4737) SS BOND : bond 0.00093 ( 3) SS BOND : angle 0.90560 ( 6) hydrogen bonds : bond 0.02150 ( 54) hydrogen bonds : angle 4.87959 ( 162) link_NAG-ASN : bond 0.00394 ( 12) link_NAG-ASN : angle 3.10732 ( 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 49 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 THR cc_start: 0.7916 (OUTLIER) cc_final: 0.7599 (p) REVERT: C 213 PHE cc_start: 0.6902 (m-10) cc_final: 0.5839 (p90) REVERT: C 227 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7813 (mmm) outliers start: 11 outliers final: 6 residues processed: 46 average time/residue: 0.3221 time to fit residues: 15.5779 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 : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 5 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 11 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN A 229 GLN B 170 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5919 r_free = 0.5919 target = 0.461210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.6801 r_free = 0.6801 target = 0.386070 restraints weight = 5358.035| |-----------------------------------------------------------------------------| r_work (start): 0.5438 rms_B_bonded: 1.17 r_work: 0.5589 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.5544 rms_B_bonded: 1.99 restraints_weight: 0.2500 r_work (final): 0.5544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3498 Z= 0.115 Angle : 0.703 10.106 4779 Z= 0.333 Chirality : 0.057 0.332 603 Planarity : 0.002 0.031 573 Dihedral : 14.387 108.498 702 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.70 % Allowed : 23.81 % Favored : 72.49 % 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: -3.17 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 247 TYR 0.013 0.001 TYR A 143 PHE 0.005 0.001 PHE B 237 HIS 0.003 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 3483) covalent geometry : angle 0.63478 ( 4737) SS BOND : bond 0.00148 ( 3) SS BOND : angle 0.85880 ( 6) hydrogen bonds : bond 0.02219 ( 54) hydrogen bonds : angle 4.89612 ( 162) link_NAG-ASN : bond 0.00444 ( 12) link_NAG-ASN : angle 3.52154 ( 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 49 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 THR cc_start: 0.8306 (OUTLIER) cc_final: 0.8095 (p) REVERT: C 213 PHE cc_start: 0.7226 (m-10) cc_final: 0.6189 (p90) outliers start: 14 outliers final: 7 residues processed: 46 average time/residue: 0.3330 time to fit residues: 16.0272 Evaluate side-chains 41 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 215 THR 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 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: 8.9990 chunk 9 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 0.0670 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN B 170 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5482 r_free = 0.5482 target = 0.193667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5304 r_free = 0.5304 target = 0.173558 restraints weight = 4819.151| |-----------------------------------------------------------------------------| r_work (start): 0.5212 rms_B_bonded: 3.36 r_work: 0.5099 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.5099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3498 Z= 0.150 Angle : 0.755 10.647 4779 Z= 0.358 Chirality : 0.058 0.372 603 Planarity : 0.003 0.032 573 Dihedral : 14.471 108.222 702 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.70 % Allowed : 24.07 % 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: -3.30 (0.35), 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 247 TYR 0.014 0.002 TYR A 143 PHE 0.006 0.001 PHE C 171 HIS 0.003 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 3483) covalent geometry : angle 0.67378 ( 4737) SS BOND : bond 0.00167 ( 3) SS BOND : angle 1.14422 ( 6) hydrogen bonds : bond 0.02450 ( 54) hydrogen bonds : angle 5.00668 ( 162) link_NAG-ASN : bond 0.00448 ( 12) link_NAG-ASN : angle 3.96971 ( 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 48 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 THR cc_start: 0.7889 (OUTLIER) cc_final: 0.7538 (p) REVERT: C 213 PHE cc_start: 0.6969 (m-10) cc_final: 0.5883 (p90) REVERT: C 228 MET cc_start: 0.8065 (tpt) cc_final: 0.7074 (tpt) outliers start: 14 outliers final: 8 residues processed: 45 average time/residue: 0.3886 time to fit residues: 18.2972 Evaluate side-chains 41 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 215 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 19 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN B 170 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5862 r_free = 0.5862 target = 0.450566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.6780 r_free = 0.6780 target = 0.371607 restraints weight = 5350.455| |-----------------------------------------------------------------------------| r_work (start): 0.5348 rms_B_bonded: 1.12 r_work: 0.5503 rms_B_bonded: 1.05 restraints_weight: 0.5000 r_work: 0.5455 rms_B_bonded: 1.90 restraints_weight: 0.2500 r_work (final): 0.5455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3498 Z= 0.212 Angle : 0.844 11.338 4779 Z= 0.406 Chirality : 0.061 0.438 603 Planarity : 0.003 0.031 573 Dihedral : 14.898 108.533 702 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.70 % Allowed : 24.60 % 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: -3.51 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 140 TYR 0.019 0.003 TYR B 143 PHE 0.009 0.002 PHE C 237 HIS 0.004 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 3483) covalent geometry : angle 0.75240 ( 4737) SS BOND : bond 0.00253 ( 3) SS BOND : angle 1.72339 ( 6) hydrogen bonds : bond 0.02615 ( 54) hydrogen bonds : angle 5.21996 ( 162) link_NAG-ASN : bond 0.00500 ( 12) link_NAG-ASN : angle 4.43136 ( 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 47 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 THR cc_start: 0.8220 (OUTLIER) cc_final: 0.7856 (p) REVERT: C 183 ASN cc_start: 0.6771 (m110) cc_final: 0.5620 (p0) REVERT: C 213 PHE cc_start: 0.7394 (m-10) cc_final: 0.6263 (p90) outliers start: 14 outliers final: 8 residues processed: 46 average time/residue: 0.3967 time to fit residues: 18.9963 Evaluate side-chains 41 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 3.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.5341 r_free = 0.5341 target = 0.177478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5153 r_free = 0.5153 target = 0.157971 restraints weight = 5001.967| |-----------------------------------------------------------------------------| r_work (start): 0.5143 rms_B_bonded: 3.43 r_work: 0.5033 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.5033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.5512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3498 Z= 0.180 Angle : 0.823 11.444 4779 Z= 0.390 Chirality : 0.060 0.411 603 Planarity : 0.003 0.028 573 Dihedral : 14.467 106.358 702 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.91 % Allowed : 26.72 % Favored : 70.37 % 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: -3.61 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 140 TYR 0.019 0.003 TYR B 143 PHE 0.008 0.001 PHE B 171 HIS 0.004 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 3483) covalent geometry : angle 0.73424 ( 4737) SS BOND : bond 0.00118 ( 3) SS BOND : angle 1.44393 ( 6) hydrogen bonds : bond 0.02506 ( 54) hydrogen bonds : angle 5.25239 ( 162) link_NAG-ASN : bond 0.00436 ( 12) link_NAG-ASN : angle 4.31479 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1214.03 seconds wall clock time: 21 minutes 30.05 seconds (1290.05 seconds total)