Starting phenix.real_space_refine on Wed Jul 23 15:15:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u10_26273/07_2025/7u10_26273.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u10_26273/07_2025/7u10_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_26273/07_2025/7u10_26273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u10_26273/07_2025/7u10_26273.map" model { file = "/net/cci-nas-00/data/ceres_data/7u10_26273/07_2025/7u10_26273.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u10_26273/07_2025/7u10_26273.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: C, B Time building chain proxies: 2.97, per 1000 atoms: 0.87 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 C 214 " - pdb=" SG CYS C 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 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: 0.86 Conformation dependent library (CDL) restraints added in 408.9 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: 0.46 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: 0.70 Time building geometry restraints manager: 1.01 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.430 Find NCS groups from input model: 0.060 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:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.120 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.002 0.001 HIS C 222 PHE 0.013 0.002 PHE A 213 TYR 0.027 0.002 TYR A 158 ARG 0.001 0.000 ARG B 247 Details of bonding type rmsd link_NAG-ASN : bond 0.00488 ( 12) link_NAG-ASN : angle 3.26437 ( 36) hydrogen bonds : bond 0.15669 ( 54) hydrogen bonds : angle 8.70705 ( 162) SS BOND : bond 0.00043 ( 3) SS BOND : angle 2.89744 ( 6) covalent geometry : bond 0.00433 ( 3483) covalent geometry : angle 0.63816 ( 4737) *********************** 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 : 0.407 Fit side-chains revert: symmetry clash REVERT: B 234 THR cc_start: 0.7622 (t) cc_final: 0.7406 (t) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.6262 time to fit residues: 51.0349 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 : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 0.0170 chunk 19 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 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 = 0.5565 r_free = 0.5565 target = 0.202987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5375 r_free = 0.5375 target = 0.180819 restraints weight = 4547.706| |-----------------------------------------------------------------------------| r_work (start): 0.5359 rms_B_bonded: 3.47 r_work: 0.5250 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.5250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3498 Z= 0.192 Angle : 0.817 12.090 4779 Z= 0.393 Chirality : 0.059 0.430 603 Planarity : 0.003 0.023 573 Dihedral : 15.897 116.853 702 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.97 % Allowed : 14.81 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 239 PHE 0.012 0.002 PHE C 237 TYR 0.016 0.003 TYR A 143 ARG 0.001 0.000 ARG A 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 12) link_NAG-ASN : angle 4.79374 ( 36) hydrogen bonds : bond 0.03207 ( 54) hydrogen bonds : angle 5.67061 ( 162) SS BOND : bond 0.00394 ( 3) SS BOND : angle 1.69524 ( 6) covalent geometry : bond 0.00429 ( 3483) covalent geometry : angle 0.70334 ( 4737) *********************** 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 63 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 SER cc_start: 0.7767 (t) cc_final: 0.7263 (t) REVERT: A 168 GLN cc_start: 0.6986 (tt0) cc_final: 0.6580 (tt0) REVERT: A 185 THR cc_start: 0.7839 (OUTLIER) cc_final: 0.7462 (p) REVERT: C 234 THR cc_start: 0.8582 (t) cc_final: 0.8296 (m) outliers start: 15 outliers final: 6 residues processed: 57 average time/residue: 0.9178 time to fit residues: 54.5195 Evaluate side-chains 48 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 A residue 240 SER Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 215 THR 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 22 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 37 optimal weight: 0.0670 chunk 32 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.5122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 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 = 0.5548 r_free = 0.5548 target = 0.202512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5360 r_free = 0.5360 target = 0.180740 restraints weight = 4592.321| |-----------------------------------------------------------------------------| r_work (start): 0.5350 rms_B_bonded: 3.45 r_work: 0.5244 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.5244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3498 Z= 0.140 Angle : 0.678 8.364 4779 Z= 0.331 Chirality : 0.056 0.352 603 Planarity : 0.002 0.013 573 Dihedral : 15.800 112.869 702 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.29 % Allowed : 16.93 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 239 PHE 0.011 0.002 PHE B 237 TYR 0.013 0.002 TYR A 143 ARG 0.001 0.000 ARG A 247 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 12) link_NAG-ASN : angle 3.68207 ( 36) hydrogen bonds : bond 0.02871 ( 54) hydrogen bonds : angle 5.35246 ( 162) SS BOND : bond 0.00568 ( 3) SS BOND : angle 1.33334 ( 6) covalent geometry : bond 0.00311 ( 3483) covalent geometry : angle 0.59828 ( 4737) *********************** 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 58 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 38 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 SER cc_start: 0.7844 (t) cc_final: 0.7577 (t) REVERT: A 161 GLU cc_start: 0.7000 (mm-30) cc_final: 0.6632 (mp0) REVERT: A 185 THR cc_start: 0.7809 (OUTLIER) cc_final: 0.7387 (p) outliers start: 20 outliers final: 8 residues processed: 53 average time/residue: 0.7973 time to fit residues: 44.2778 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 : 0.388 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 5.9990 chunk 33 optimal weight: 0.0570 chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5922 r_free = 0.5922 target = 0.460410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.6788 r_free = 0.6788 target = 0.384416 restraints weight = 5277.428| |-----------------------------------------------------------------------------| r_work (start): 0.5220 rms_B_bonded: 1.14 r_work: 0.5125 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.5059 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.5059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3498 Z= 0.165 Angle : 0.726 8.749 4779 Z= 0.356 Chirality : 0.059 0.389 603 Planarity : 0.002 0.015 573 Dihedral : 16.030 117.020 702 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.29 % Allowed : 19.58 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 239 PHE 0.007 0.002 PHE C 171 TYR 0.022 0.002 TYR A 143 ARG 0.001 0.000 ARG A 140 Details of bonding type rmsd link_NAG-ASN : bond 0.00378 ( 12) link_NAG-ASN : angle 3.83439 ( 36) hydrogen bonds : bond 0.02779 ( 54) hydrogen bonds : angle 5.26038 ( 162) SS BOND : bond 0.00030 ( 3) SS BOND : angle 1.37707 ( 6) covalent geometry : bond 0.00377 ( 3483) covalent geometry : angle 0.64600 ( 4737) *********************** 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 59 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 39 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 GLU cc_start: 0.7114 (mm-30) cc_final: 0.6791 (mp0) REVERT: A 185 THR cc_start: 0.7797 (OUTLIER) cc_final: 0.7373 (p) REVERT: B 210 MET cc_start: 0.6704 (mtp) cc_final: 0.6014 (mtt) REVERT: C 135 TYR cc_start: 0.7293 (OUTLIER) cc_final: 0.6855 (m-10) REVERT: C 234 THR cc_start: 0.8594 (t) cc_final: 0.8332 (m) outliers start: 20 outliers final: 9 residues processed: 52 average time/residue: 0.6619 time to fit residues: 36.4632 Evaluate side-chains 48 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 234 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 253 CYS 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.0170 chunk 11 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5590 r_free = 0.5590 target = 0.205347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5404 r_free = 0.5404 target = 0.183752 restraints weight = 4670.307| |-----------------------------------------------------------------------------| r_work (start): 0.5299 rms_B_bonded: 3.50 r_work: 0.5187 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.5187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3498 Z= 0.103 Angle : 0.641 8.043 4779 Z= 0.311 Chirality : 0.056 0.310 603 Planarity : 0.002 0.008 573 Dihedral : 15.166 111.362 702 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.17 % Allowed : 23.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 239 PHE 0.005 0.001 PHE B 237 TYR 0.015 0.001 TYR A 143 ARG 0.001 0.000 ARG C 140 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 12) link_NAG-ASN : angle 2.98750 ( 36) hydrogen bonds : bond 0.02469 ( 54) hydrogen bonds : angle 5.15116 ( 162) SS BOND : bond 0.00131 ( 3) SS BOND : angle 0.97049 ( 6) covalent geometry : bond 0.00226 ( 3483) covalent geometry : angle 0.58827 ( 4737) *********************** 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 52 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 THR cc_start: 0.7858 (OUTLIER) cc_final: 0.7528 (p) REVERT: B 210 MET cc_start: 0.6672 (mtp) cc_final: 0.6048 (mtt) REVERT: C 234 THR cc_start: 0.8621 (t) cc_final: 0.8360 (m) outliers start: 12 outliers final: 6 residues processed: 47 average time/residue: 0.7731 time to fit residues: 38.3154 Evaluate side-chains 41 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 253 CYS 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 8 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 36 optimal weight: 0.1980 chunk 4 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5475 r_free = 0.5475 target = 0.193032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.5285 r_free = 0.5285 target = 0.172792 restraints weight = 4960.354| |-----------------------------------------------------------------------------| r_work (start): 0.5193 rms_B_bonded: 3.45 r_work: 0.5088 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.5088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3498 Z= 0.169 Angle : 0.729 9.216 4779 Z= 0.353 Chirality : 0.059 0.378 603 Planarity : 0.002 0.015 573 Dihedral : 15.272 108.339 702 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.97 % Allowed : 23.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 239 PHE 0.007 0.001 PHE C 171 TYR 0.017 0.002 TYR A 143 ARG 0.001 0.000 ARG A 140 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 12) link_NAG-ASN : angle 3.64988 ( 36) hydrogen bonds : bond 0.02450 ( 54) hydrogen bonds : angle 5.19436 ( 162) SS BOND : bond 0.00198 ( 3) SS BOND : angle 1.00111 ( 6) covalent geometry : bond 0.00383 ( 3483) covalent geometry : angle 0.65851 ( 4737) *********************** 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 45 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 30 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 THR cc_start: 0.7889 (OUTLIER) cc_final: 0.7535 (p) REVERT: B 210 MET cc_start: 0.6749 (mtp) cc_final: 0.6462 (mtp) REVERT: B 234 THR cc_start: 0.8144 (OUTLIER) cc_final: 0.7900 (m) REVERT: C 213 PHE cc_start: 0.6772 (m-10) cc_final: 0.5673 (p90) outliers start: 15 outliers final: 7 residues processed: 40 average time/residue: 0.7794 time to fit residues: 32.9120 Evaluate side-chains 39 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 B residue 234 THR Chi-restraints excluded: chain B residue 253 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.5906 r_free = 0.5906 target = 0.457557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.6785 r_free = 0.6785 target = 0.380902 restraints weight = 5293.641| |-----------------------------------------------------------------------------| r_work (start): 0.5213 rms_B_bonded: 1.15 r_work: 0.5122 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.5058 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.5058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3498 Z= 0.158 Angle : 0.722 8.713 4779 Z= 0.349 Chirality : 0.059 0.372 603 Planarity : 0.002 0.012 573 Dihedral : 15.116 107.340 702 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.97 % Allowed : 24.07 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 239 PHE 0.008 0.001 PHE A 237 TYR 0.016 0.002 TYR A 143 ARG 0.001 0.000 ARG A 140 Details of bonding type rmsd link_NAG-ASN : bond 0.00440 ( 12) link_NAG-ASN : angle 3.54423 ( 36) hydrogen bonds : bond 0.02328 ( 54) hydrogen bonds : angle 5.23538 ( 162) SS BOND : bond 0.00231 ( 3) SS BOND : angle 0.85262 ( 6) covalent geometry : bond 0.00360 ( 3483) covalent geometry : angle 0.65571 ( 4737) *********************** 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 52 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 THR cc_start: 0.7897 (OUTLIER) cc_final: 0.7495 (p) REVERT: C 213 PHE cc_start: 0.6934 (m-10) cc_final: 0.5838 (p90) REVERT: C 234 THR cc_start: 0.8738 (t) cc_final: 0.8451 (m) outliers start: 15 outliers final: 7 residues processed: 49 average time/residue: 0.7694 time to fit residues: 39.6336 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 : 0.352 ------------------------------------------------------------------------------- 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 B residue 253 CYS 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 9 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 C 168 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5902 r_free = 0.5902 target = 0.456800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.6789 r_free = 0.6789 target = 0.379905 restraints weight = 5332.764| |-----------------------------------------------------------------------------| r_work (start): 0.5416 rms_B_bonded: 1.16 r_work: 0.5567 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.5516 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work (final): 0.5516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.4889 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= 0.159 Angle : 0.731 9.007 4779 Z= 0.353 Chirality : 0.059 0.376 603 Planarity : 0.002 0.030 573 Dihedral : 14.992 106.581 702 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.23 % Allowed : 24.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 239 PHE 0.007 0.001 PHE C 171 TYR 0.015 0.002 TYR A 143 ARG 0.001 0.000 ARG A 140 Details of bonding type rmsd link_NAG-ASN : bond 0.00411 ( 12) link_NAG-ASN : angle 3.52165 ( 36) hydrogen bonds : bond 0.02286 ( 54) hydrogen bonds : angle 5.25870 ( 162) SS BOND : bond 0.00232 ( 3) SS BOND : angle 0.84711 ( 6) covalent geometry : bond 0.00361 ( 3483) covalent geometry : angle 0.66651 ( 4737) *********************** 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: 16 poor density : 34 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 THR cc_start: 0.8206 (OUTLIER) cc_final: 0.7922 (p) REVERT: B 210 MET cc_start: 0.7201 (mtp) cc_final: 0.6841 (mtp) REVERT: C 213 PHE cc_start: 0.7277 (m-10) cc_final: 0.6190 (p90) outliers start: 16 outliers final: 8 residues processed: 47 average time/residue: 0.7516 time to fit residues: 37.1812 Evaluate side-chains 43 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 B residue 253 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 34 optimal weight: 0.2980 chunk 33 optimal weight: 30.0000 chunk 37 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 0.2980 chunk 21 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5569 r_free = 0.5569 target = 0.203036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5386 r_free = 0.5386 target = 0.182089 restraints weight = 4558.914| |-----------------------------------------------------------------------------| r_work (start): 0.5286 rms_B_bonded: 3.42 r_work: 0.5175 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.5175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.4882 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= 0.102 Angle : 0.674 9.255 4779 Z= 0.321 Chirality : 0.056 0.302 603 Planarity : 0.002 0.029 573 Dihedral : 14.350 103.577 702 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.91 % Allowed : 25.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 239 PHE 0.006 0.001 PHE C 237 TYR 0.010 0.001 TYR A 143 ARG 0.001 0.000 ARG A 247 Details of bonding type rmsd link_NAG-ASN : bond 0.00398 ( 12) link_NAG-ASN : angle 2.97024 ( 36) hydrogen bonds : bond 0.02185 ( 54) hydrogen bonds : angle 5.12648 ( 162) SS BOND : bond 0.00166 ( 3) SS BOND : angle 0.63931 ( 6) covalent geometry : bond 0.00222 ( 3483) covalent geometry : angle 0.62458 ( 4737) *********************** 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 47 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 THR cc_start: 0.8095 (OUTLIER) cc_final: 0.7868 (p) REVERT: B 210 MET cc_start: 0.6684 (mtp) cc_final: 0.6007 (mtt) REVERT: C 213 PHE cc_start: 0.6837 (m-10) cc_final: 0.5802 (p90) REVERT: C 253 CYS cc_start: 0.7236 (OUTLIER) cc_final: 0.6738 (m) outliers start: 11 outliers final: 6 residues processed: 44 average time/residue: 0.7567 time to fit residues: 35.0614 Evaluate side-chains 43 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 253 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.0060 chunk 27 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- 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 245 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 = 0.5530 r_free = 0.5530 target = 0.198971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5340 r_free = 0.5340 target = 0.177761 restraints weight = 4745.241| |-----------------------------------------------------------------------------| r_work (start): 0.5246 rms_B_bonded: 3.50 r_work: 0.5131 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.5131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3498 Z= 0.120 Angle : 0.692 9.505 4779 Z= 0.331 Chirality : 0.057 0.322 603 Planarity : 0.002 0.030 573 Dihedral : 14.264 104.012 702 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.65 % Allowed : 25.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 239 PHE 0.005 0.001 PHE C 237 TYR 0.016 0.002 TYR C 250 ARG 0.001 0.000 ARG A 247 Details of bonding type rmsd link_NAG-ASN : bond 0.00366 ( 12) link_NAG-ASN : angle 3.03928 ( 36) hydrogen bonds : bond 0.02156 ( 54) hydrogen bonds : angle 5.08046 ( 162) SS BOND : bond 0.00181 ( 3) SS BOND : angle 0.82985 ( 6) covalent geometry : bond 0.00269 ( 3483) covalent geometry : angle 0.64161 ( 4737) ********************** 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 45 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 THR cc_start: 0.8048 (OUTLIER) cc_final: 0.7753 (p) REVERT: B 210 MET cc_start: 0.6858 (mtp) cc_final: 0.6273 (mtp) REVERT: C 213 PHE cc_start: 0.6870 (m-10) cc_final: 0.5881 (p90) outliers start: 10 outliers final: 7 residues processed: 42 average time/residue: 0.7387 time to fit residues: 32.8123 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 : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 253 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 2 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 30 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 245 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 = 0.5458 r_free = 0.5458 target = 0.191465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5273 r_free = 0.5273 target = 0.171276 restraints weight = 4838.851| |-----------------------------------------------------------------------------| r_work (start): 0.5309 rms_B_bonded: 3.36 r_work: 0.5222 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.5222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6084 moved from start: 0.5163 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= 0.158 Angle : 0.740 9.486 4779 Z= 0.358 Chirality : 0.059 0.380 603 Planarity : 0.003 0.033 573 Dihedral : 14.676 106.261 702 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.91 % Allowed : 25.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 239 PHE 0.006 0.001 PHE C 171 TYR 0.018 0.002 TYR B 143 ARG 0.001 0.000 ARG A 247 Details of bonding type rmsd link_NAG-ASN : bond 0.00409 ( 12) link_NAG-ASN : angle 3.43484 ( 36) hydrogen bonds : bond 0.02261 ( 54) hydrogen bonds : angle 5.19145 ( 162) SS BOND : bond 0.00247 ( 3) SS BOND : angle 0.81033 ( 6) covalent geometry : bond 0.00361 ( 3483) covalent geometry : angle 0.68010 ( 4737) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2649.86 seconds wall clock time: 46 minutes 15.65 seconds (2775.65 seconds total)