Starting phenix.real_space_refine on Wed Sep 17 03:58:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u14_26277/09_2025/7u14_26277.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u14_26277/09_2025/7u14_26277.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7u14_26277/09_2025/7u14_26277.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u14_26277/09_2025/7u14_26277.map" model { file = "/net/cci-nas-00/data/ceres_data/7u14_26277/09_2025/7u14_26277.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u14_26277/09_2025/7u14_26277.cif" } resolution = 4.5 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= 0.003 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 2202 2.51 5 N 531 2.21 5 O 702 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3456 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1096 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 135, 1087 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 132} Conformer: "B" Number of residues, atoms: 135, 1087 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 132} bond proxies already assigned to first conformer: 1094 Chain: "B" Number of atoms: 1096 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 135, 1087 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 132} Conformer: "B" Number of residues, atoms: 135, 1087 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 132} bond proxies already assigned to first conformer: 1094 Chain: "C" Number of atoms: 1096 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 135, 1087 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 132} Conformer: "B" Number of residues, atoms: 135, 1087 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 132} bond proxies already assigned to first conformer: 1094 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 Chain: "B" 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 Chain: "C" 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 Time building chain proxies: 1.87, per 1000 atoms: 0.54 Number of scatterers: 3456 At special positions: 0 Unit cell: (98.808, 118.14, 33.294, 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 702 8.00 N 531 7.00 C 2202 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=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 253 " distance=2.04 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: 0.29 Conformation dependent library (CDL) restraints added in 241.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 60.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 137 removed outlier: 6.384A pdb=" N LYS A 129 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N TYR B 132 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N ALA A 131 " --> pdb=" O TYR B 132 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N SER B 134 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 9.124A pdb=" N VAL A 133 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 9.683A pdb=" N ASP B 136 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N TYR A 135 " --> pdb=" O ASP B 136 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LYS B 129 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N TYR C 132 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N ALA B 131 " --> pdb=" O TYR C 132 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N SER C 134 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N VAL B 133 " --> pdb=" O SER C 134 " (cutoff:3.500A) removed outlier: 9.677A pdb=" N ASP C 136 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 8.826A 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 141 through 165 removed outlier: 6.948A pdb=" N ILE A 146 " --> pdb=" O ASN B 145 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N THR B 147 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ASN A 148 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N THR B 149 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU A 150 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ASN B 151 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE A 152 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N THR B 153 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASN A 154 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ASN B 155 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ASN A 156 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N TYR B 157 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR A 158 " --> pdb=" O TYR B 157 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N SER B 159 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL A 160 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLU B 161 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE B 146 " --> pdb=" O ASN C 145 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR C 147 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 7.025A 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: 6.996A pdb=" N LEU B 150 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASN C 151 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE B 152 " --> pdb=" O ASN C 151 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N THR C 153 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASN B 154 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASN C 155 " --> pdb=" O ASN B 154 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASN B 156 " --> pdb=" O ASN C 155 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N TYR C 157 " --> pdb=" O ASN B 156 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N TYR B 158 " --> pdb=" O TYR C 157 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N SER C 159 " --> pdb=" O TYR B 158 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B 160 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLU C 161 " --> pdb=" O VAL B 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 168 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 181 removed outlier: 6.575A pdb=" N ARG A 180 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ARG B 180 " --> pdb=" O LEU C 181 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 184 through 187 removed outlier: 6.408A pdb=" N THR A 185 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR B 185 " --> pdb=" O ILE C 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 191 through 198 removed outlier: 6.775A pdb=" N ILE A 195 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASP B 196 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TYR A 197 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR B 198 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE B 195 " --> pdb=" O GLN C 194 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASP C 196 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TYR B 197 " --> pdb=" O ASP C 196 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N THR C 198 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.336A pdb=" N VAL A 202 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL B 202 " --> pdb=" O ILE C 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 209 through 219 removed outlier: 6.973A pdb=" N MET A 210 " --> pdb=" O TYR B 209 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N TYR B 211 " --> pdb=" O MET A 210 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASP A 212 " --> pdb=" O TYR B 211 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE B 213 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N MET B 210 " --> pdb=" O TYR C 209 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N TYR C 211 " --> pdb=" O MET B 210 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ASP B 212 " --> pdb=" O TYR C 211 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N PHE C 213 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 225 through 228 Processing sheet with id=AB2, first strand: chain 'A' and resid 233 through 245 removed outlier: 6.605A pdb=" N THR A 234 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N PHE B 237 " --> pdb=" O THR A 234 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TYR A 236 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N HIS B 239 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLY A 238 " --> pdb=" O HIS B 239 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N GLU B 241 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER A 240 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ILE B 243 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLN A 242 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLN B 245 " --> pdb=" O GLN A 242 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER A 244 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR B 234 " --> pdb=" O THR C 235 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N PHE C 237 " --> pdb=" O THR B 234 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR B 236 " --> pdb=" O PHE C 237 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N HIS C 239 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY B 238 " --> pdb=" O HIS C 239 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N GLU C 241 " --> pdb=" O GLY B 238 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N SER B 240 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N ILE C 243 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLN B 242 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLN C 245 " --> pdb=" O GLN B 242 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N SER B 244 " --> pdb=" O GLN C 245 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 251 through 253 66 hydrogen bonds defined for protein. 198 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: 0.58 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1011 1.34 - 1.46: 629 1.46 - 1.58: 1840 1.58 - 1.70: 0 1.70 - 1.82: 36 Bond restraints: 3516 Sorted by residual: bond pdb=" C1 NAG A 304 " pdb=" O5 NAG A 304 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C1 NAG C 304 " pdb=" O5 NAG C 304 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C1 NAG B 304 " pdb=" O5 NAG B 304 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" CD GLU A 206 " pdb=" OE1 GLU A 206 " ideal model delta sigma weight residual 1.249 1.214 0.035 1.90e-02 2.77e+03 3.39e+00 bond pdb=" CB VAL C 225 " pdb=" CG2 VAL C 225 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.33e+00 ... (remaining 3511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 4465 1.69 - 3.38: 260 3.38 - 5.07: 42 5.07 - 6.76: 12 6.76 - 8.45: 9 Bond angle restraints: 4788 Sorted by residual: angle pdb=" CA MET C 228 " pdb=" CB MET C 228 " pdb=" CG MET C 228 " ideal model delta sigma weight residual 114.10 121.52 -7.42 2.00e+00 2.50e-01 1.38e+01 angle pdb=" CA MET A 228 " pdb=" CB MET A 228 " pdb=" CG MET A 228 " ideal model delta sigma weight residual 114.10 121.51 -7.41 2.00e+00 2.50e-01 1.37e+01 angle pdb=" CA MET B 228 " pdb=" CB MET B 228 " pdb=" CG MET B 228 " ideal model delta sigma weight residual 114.10 121.42 -7.32 2.00e+00 2.50e-01 1.34e+01 angle pdb=" CA GLU C 205 " pdb=" CB GLU C 205 " pdb=" CG GLU C 205 " ideal model delta sigma weight residual 114.10 121.18 -7.08 2.00e+00 2.50e-01 1.25e+01 angle pdb=" CA GLU B 205 " pdb=" CB GLU B 205 " pdb=" CG GLU B 205 " ideal model delta sigma weight residual 114.10 121.12 -7.02 2.00e+00 2.50e-01 1.23e+01 ... (remaining 4783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.61: 2043 24.61 - 49.21: 178 49.21 - 73.82: 29 73.82 - 98.43: 18 98.43 - 123.04: 3 Dihedral angle restraints: 2271 sinusoidal: 1038 harmonic: 1233 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 93.00 40.17 52.83 1 1.00e+01 1.00e-02 3.80e+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 93.00 40.18 52.82 1 1.00e+01 1.00e-02 3.80e+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 93.00 40.24 52.76 1 1.00e+01 1.00e-02 3.79e+01 ... (remaining 2268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 477 0.078 - 0.156: 117 0.156 - 0.234: 9 0.234 - 0.312: 0 0.312 - 0.390: 3 Chirality restraints: 606 Sorted by residual: chirality pdb=" CB ILE C 203 " pdb=" CA ILE C 203 " pdb=" CG1 ILE C 203 " pdb=" CG2 ILE C 203 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CB ILE A 203 " pdb=" CA ILE A 203 " pdb=" CG1 ILE A 203 " pdb=" CG2 ILE A 203 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CB ILE B 203 " pdb=" CA ILE B 203 " pdb=" CG1 ILE B 203 " pdb=" CG2 ILE B 203 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.66e+00 ... (remaining 603 not shown) Planarity restraints: 591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 125 " -0.027 2.00e-02 2.50e+03 2.67e-02 1.43e+01 pdb=" CG TYR C 125 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR C 125 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR C 125 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR C 125 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR C 125 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR C 125 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 125 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 125 " -0.027 2.00e-02 2.50e+03 2.66e-02 1.42e+01 pdb=" CG TYR A 125 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR A 125 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 125 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR A 125 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR A 125 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 125 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 125 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 125 " -0.026 2.00e-02 2.50e+03 2.65e-02 1.41e+01 pdb=" CG TYR B 125 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR B 125 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 125 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR B 125 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR B 125 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 125 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 125 " 0.000 2.00e-02 2.50e+03 ... (remaining 588 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 1220 2.87 - 3.38: 2979 3.38 - 3.89: 6107 3.89 - 4.39: 6044 4.39 - 4.90: 11905 Nonbonded interactions: 28255 Sorted by model distance: nonbonded pdb=" NZ LYS C 129 " pdb=" OD2 ASP C 136 " model vdw 2.369 3.120 nonbonded pdb=" NZ LYS B 129 " pdb=" OD2 ASP B 136 " model vdw 2.369 3.120 nonbonded pdb=" NZ LYS A 129 " pdb=" OD2 ASP A 136 " model vdw 2.370 3.120 nonbonded pdb=" OH TYR B 236 " pdb=" O HIS B 239 " model vdw 2.423 3.040 nonbonded pdb=" OH TYR A 236 " pdb=" O HIS A 239 " model vdw 2.424 3.040 ... (remaining 28250 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 Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.060 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.070 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5068 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 : 0.006 0.074 3531 Z= 0.290 Angle : 0.962 8.455 4830 Z= 0.496 Chirality : 0.066 0.390 606 Planarity : 0.005 0.028 579 Dihedral : 19.585 123.035 1476 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 6.30 % Allowed : 2.36 % Favored : 91.34 % 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 aren not related in a simple way. whole: -3.07 (0.38), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 247 TYR 0.064 0.004 TYR C 125 PHE 0.020 0.004 PHE B 171 HIS 0.002 0.001 HIS C 222 Details of bonding type rmsd covalent geometry : bond 0.00637 ( 3516) covalent geometry : angle 0.94464 ( 4788) SS BOND : bond 0.00725 ( 3) SS BOND : angle 2.35437 ( 6) hydrogen bonds : bond 0.13721 ( 66) hydrogen bonds : angle 8.52990 ( 198) link_NAG-ASN : bond 0.00574 ( 12) link_NAG-ASN : angle 2.12511 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.048 Fit side-chains REVERT: A 171 PHE cc_start: 0.7517 (t80) cc_final: 0.6047 (p90) REVERT: A 213 PHE cc_start: 0.6519 (t80) cc_final: 0.4232 (p90) REVERT: A 222 HIS cc_start: 0.6925 (m-70) cc_final: 0.5425 (p90) REVERT: A 223 ASN cc_start: 0.4231 (OUTLIER) cc_final: 0.4021 (p0) outliers start: 8 outliers final: 0 residues processed: 25 average time/residue: 0.0407 time to fit residues: 1.1905 Evaluate side-chains 15 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.044 ------------------------------------------------------------------------------- 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: 10.0000 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.0020 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 overall best weight: 2.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5233 r_free = 0.5233 target = 0.336249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.5313 r_free = 0.5313 target = 0.281894 restraints weight = 12047.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.5369 r_free = 0.5369 target = 0.277910 restraints weight = 5411.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.5372 r_free = 0.5372 target = 0.277317 restraints weight = 4038.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.5430 r_free = 0.5430 target = 0.273920 restraints weight = 3415.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.5453 r_free = 0.5453 target = 0.271771 restraints weight = 4014.114| |-----------------------------------------------------------------------------| r_work (final): 0.5160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5161 r_free = 0.5161 target_work(ls_wunit_k1) = 0.309 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5164 r_free = 0.5164 target_work(ls_wunit_k1) = 0.309 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.5164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5385 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3531 Z= 0.173 Angle : 0.849 8.291 4830 Z= 0.427 Chirality : 0.067 0.442 606 Planarity : 0.003 0.021 579 Dihedral : 13.930 102.906 711 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.79 % Allowed : 4.72 % Favored : 94.49 % 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 aren not related in a simple way. whole: -3.42 (0.37), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 247 TYR 0.012 0.002 TYR A 143 PHE 0.009 0.002 PHE B 237 HIS 0.006 0.003 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 3516) covalent geometry : angle 0.81161 ( 4788) SS BOND : bond 0.00727 ( 3) SS BOND : angle 2.69539 ( 6) hydrogen bonds : bond 0.07746 ( 66) hydrogen bonds : angle 6.40619 ( 198) link_NAG-ASN : bond 0.00667 ( 12) link_NAG-ASN : angle 2.82241 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.044 Fit side-chains REVERT: C 207 MET cc_start: 0.3219 (ptm) cc_final: 0.2625 (tpt) outliers start: 1 outliers final: 0 residues processed: 17 average time/residue: 0.0283 time to fit residues: 0.6256 Evaluate side-chains 10 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 2 optimal weight: 0.0980 chunk 11 optimal weight: 9.9990 chunk 15 optimal weight: 0.0070 chunk 31 optimal weight: 5.9990 chunk 14 optimal weight: 0.0870 chunk 8 optimal weight: 0.8980 chunk 17 optimal weight: 0.0270 chunk 22 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 overall best weight: 0.2234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 HIS C 239 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5270 r_free = 0.5270 target = 0.350620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5375 r_free = 0.5375 target = 0.294335 restraints weight = 12144.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.5413 r_free = 0.5413 target = 0.293118 restraints weight = 5777.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.5452 r_free = 0.5452 target = 0.291759 restraints weight = 4171.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.5470 r_free = 0.5470 target = 0.291364 restraints weight = 3966.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.5474 r_free = 0.5474 target = 0.290845 restraints weight = 3926.002| |-----------------------------------------------------------------------------| r_work (final): 0.5182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5183 r_free = 0.5183 target_work(ls_wunit_k1) = 0.322 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5183 r_free = 0.5183 target_work(ls_wunit_k1) = 0.322 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.5183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5244 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3531 Z= 0.147 Angle : 0.871 8.992 4830 Z= 0.420 Chirality : 0.067 0.419 606 Planarity : 0.003 0.021 579 Dihedral : 13.416 104.424 711 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.79 % Allowed : 1.57 % Favored : 97.64 % 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 aren not related in a simple way. whole: -3.40 (0.37), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 180 TYR 0.012 0.001 TYR A 143 PHE 0.011 0.002 PHE C 237 HIS 0.006 0.002 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 3516) covalent geometry : angle 0.79323 ( 4788) SS BOND : bond 0.00161 ( 3) SS BOND : angle 1.92652 ( 6) hydrogen bonds : bond 0.07079 ( 66) hydrogen bonds : angle 6.46467 ( 198) link_NAG-ASN : bond 0.00712 ( 12) link_NAG-ASN : angle 4.17367 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.045 Fit side-chains REVERT: C 140 ARG cc_start: 0.7336 (tpt90) cc_final: 0.5841 (tmt170) REVERT: C 222 HIS cc_start: 0.6845 (OUTLIER) cc_final: 0.5740 (p90) REVERT: C 229 GLN cc_start: 0.7269 (tt0) cc_final: 0.5357 (mp10) outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.0389 time to fit residues: 0.9191 Evaluate side-chains 19 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 0 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 14 optimal weight: 0.0170 chunk 24 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 overall best weight: 5.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5176 r_free = 0.5176 target = 0.343099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.5248 r_free = 0.5248 target = 0.280705 restraints weight = 5233.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.5259 r_free = 0.5259 target = 0.278900 restraints weight = 5382.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.5268 r_free = 0.5268 target = 0.277424 restraints weight = 3952.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.5268 r_free = 0.5268 target = 0.277378 restraints weight = 3807.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5269 r_free = 0.5269 target = 0.277342 restraints weight = 3255.327| |-----------------------------------------------------------------------------| r_work (final): 0.5080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5080 r_free = 0.5080 target_work(ls_wunit_k1) = 0.321 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5080 r_free = 0.5080 target_work(ls_wunit_k1) = 0.321 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.5080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5820 moved from start: 0.5440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 3531 Z= 0.209 Angle : 0.974 9.289 4830 Z= 0.477 Chirality : 0.066 0.331 606 Planarity : 0.004 0.027 579 Dihedral : 13.813 107.335 711 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.79 % Allowed : 3.94 % Favored : 95.28 % 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 aren not related in a simple way. whole: -3.63 (0.36), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 247 TYR 0.020 0.003 TYR B 143 PHE 0.006 0.002 PHE B 171 HIS 0.007 0.003 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 3516) covalent geometry : angle 0.88838 ( 4788) SS BOND : bond 0.01055 ( 3) SS BOND : angle 3.13728 ( 6) hydrogen bonds : bond 0.07150 ( 66) hydrogen bonds : angle 5.92371 ( 198) link_NAG-ASN : bond 0.00885 ( 12) link_NAG-ASN : angle 4.54557 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.077 Fit side-chains REVERT: C 140 ARG cc_start: 0.7510 (tpt90) cc_final: 0.5671 (tmt170) REVERT: C 228 MET cc_start: 0.5823 (ptm) cc_final: 0.4966 (ppp) outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.0509 time to fit residues: 1.2007 Evaluate side-chains 14 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 chunk 29 optimal weight: 0.0470 chunk 9 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 overall best weight: 5.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5093 r_free = 0.5093 target = 0.303681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.5136 r_free = 0.5136 target = 0.245315 restraints weight = 8024.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5136 r_free = 0.5136 target = 0.242795 restraints weight = 5656.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.5165 r_free = 0.5165 target = 0.238854 restraints weight = 4422.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.5170 r_free = 0.5170 target = 0.237966 restraints weight = 3692.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.5171 r_free = 0.5171 target = 0.237834 restraints weight = 4375.855| |-----------------------------------------------------------------------------| r_work (final): 0.4983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4983 r_free = 0.4983 target_work(ls_wunit_k1) = 0.277 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4983 r_free = 0.4983 target_work(ls_wunit_k1) = 0.277 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5958 moved from start: 0.6089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 3531 Z= 0.212 Angle : 1.042 8.992 4830 Z= 0.512 Chirality : 0.071 0.494 606 Planarity : 0.004 0.029 579 Dihedral : 13.962 107.695 711 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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 aren not related in a simple way. whole: -3.82 (0.36), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.90 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 247 TYR 0.016 0.003 TYR A 157 PHE 0.009 0.002 PHE C 237 HIS 0.005 0.002 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00513 ( 3516) covalent geometry : angle 0.95838 ( 4788) SS BOND : bond 0.01137 ( 3) SS BOND : angle 2.51533 ( 6) hydrogen bonds : bond 0.06824 ( 66) hydrogen bonds : angle 5.87102 ( 198) link_NAG-ASN : bond 0.00747 ( 12) link_NAG-ASN : angle 4.74027 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.036 Fit side-chains REVERT: C 228 MET cc_start: 0.6005 (ptm) cc_final: 0.4897 (ppp) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0259 time to fit residues: 0.5711 Evaluate side-chains 13 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 7 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 36 optimal weight: 0.0370 chunk 37 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 overall best weight: 2.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5113 r_free = 0.5113 target = 0.309012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.5158 r_free = 0.5158 target = 0.245588 restraints weight = 5576.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5173 r_free = 0.5173 target = 0.241187 restraints weight = 6121.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.5204 r_free = 0.5204 target = 0.235077 restraints weight = 4422.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5204 r_free = 0.5204 target = 0.235075 restraints weight = 4339.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5204 r_free = 0.5204 target = 0.235075 restraints weight = 4291.757| |-----------------------------------------------------------------------------| r_work (final): 0.4992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4992 r_free = 0.4992 target_work(ls_wunit_k1) = 0.279 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4993 r_free = 0.4993 target_work(ls_wunit_k1) = 0.279 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5851 moved from start: 0.6144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3531 Z= 0.162 Angle : 0.963 9.837 4830 Z= 0.459 Chirality : 0.075 0.642 606 Planarity : 0.003 0.030 579 Dihedral : 13.686 107.624 711 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % 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 aren not related in a simple way. whole: -3.80 (0.36), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 180 TYR 0.010 0.002 TYR A 143 PHE 0.010 0.002 PHE C 237 HIS 0.002 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 3516) covalent geometry : angle 0.89260 ( 4788) SS BOND : bond 0.00872 ( 3) SS BOND : angle 1.94596 ( 6) hydrogen bonds : bond 0.06625 ( 66) hydrogen bonds : angle 6.31965 ( 198) link_NAG-ASN : bond 0.00696 ( 12) link_NAG-ASN : angle 4.23713 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.041 Fit side-chains REVERT: C 206 GLU cc_start: 0.8207 (pm20) cc_final: 0.7900 (mm-30) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0262 time to fit residues: 0.5956 Evaluate side-chains 12 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 14 optimal weight: 0.0970 chunk 25 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 8 optimal weight: 0.4980 chunk 38 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 overall best weight: 3.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5091 r_free = 0.5091 target = 0.305606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.5132 r_free = 0.5132 target = 0.247885 restraints weight = 6059.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.5153 r_free = 0.5153 target = 0.244299 restraints weight = 5312.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5156 r_free = 0.5156 target = 0.243479 restraints weight = 4624.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.5181 r_free = 0.5181 target = 0.239497 restraints weight = 4064.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.5186 r_free = 0.5186 target = 0.239005 restraints weight = 4287.593| |-----------------------------------------------------------------------------| r_work (final): 0.5000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5000 r_free = 0.5000 target_work(ls_wunit_k1) = 0.281 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5000 r_free = 0.5000 target_work(ls_wunit_k1) = 0.281 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.5000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5824 moved from start: 0.6493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3531 Z= 0.165 Angle : 0.914 7.882 4830 Z= 0.447 Chirality : 0.065 0.404 606 Planarity : 0.003 0.029 579 Dihedral : 13.543 106.924 711 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.80 (0.36), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 247 TYR 0.012 0.002 TYR B 143 PHE 0.011 0.002 PHE B 237 HIS 0.002 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 3516) covalent geometry : angle 0.83946 ( 4788) SS BOND : bond 0.00928 ( 3) SS BOND : angle 1.94018 ( 6) hydrogen bonds : bond 0.06463 ( 66) hydrogen bonds : angle 6.23161 ( 198) link_NAG-ASN : bond 0.00680 ( 12) link_NAG-ASN : angle 4.21252 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.048 Fit side-chains REVERT: C 206 GLU cc_start: 0.8079 (pm20) cc_final: 0.7835 (mm-30) REVERT: C 228 MET cc_start: 0.6338 (ptm) cc_final: 0.5542 (ppp) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0286 time to fit residues: 0.6374 Evaluate side-chains 13 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 ASN C 239 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5117 r_free = 0.5117 target = 0.329271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.5188 r_free = 0.5188 target = 0.270262 restraints weight = 5672.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.5214 r_free = 0.5214 target = 0.264445 restraints weight = 5087.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.5223 r_free = 0.5223 target = 0.262453 restraints weight = 3891.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.5223 r_free = 0.5223 target = 0.262443 restraints weight = 3360.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5223 r_free = 0.5223 target = 0.262410 restraints weight = 3097.218| |-----------------------------------------------------------------------------| r_work (final): 0.5035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5035 r_free = 0.5035 target_work(ls_wunit_k1) = 0.304 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5035 r_free = 0.5035 target_work(ls_wunit_k1) = 0.304 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.5035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5946 moved from start: 0.7001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 3531 Z= 0.205 Angle : 0.991 8.463 4830 Z= 0.484 Chirality : 0.074 0.600 606 Planarity : 0.004 0.029 579 Dihedral : 13.838 107.739 711 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % 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 aren not related in a simple way. whole: -3.87 (0.36), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 180 TYR 0.028 0.003 TYR C 236 PHE 0.005 0.002 PHE A 237 HIS 0.004 0.002 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00523 ( 3516) covalent geometry : angle 0.91201 ( 4788) SS BOND : bond 0.01247 ( 3) SS BOND : angle 2.50237 ( 6) hydrogen bonds : bond 0.06649 ( 66) hydrogen bonds : angle 6.44889 ( 198) link_NAG-ASN : bond 0.00698 ( 12) link_NAG-ASN : angle 4.48838 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.037 Fit side-chains REVERT: C 125 TYR cc_start: 0.6711 (t80) cc_final: 0.5720 (m-80) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0280 time to fit residues: 0.5477 Evaluate side-chains 13 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5113 r_free = 0.5113 target = 0.307422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.5168 r_free = 0.5168 target = 0.245820 restraints weight = 5598.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.5175 r_free = 0.5175 target = 0.243716 restraints weight = 6256.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.5185 r_free = 0.5185 target = 0.242103 restraints weight = 5351.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.5188 r_free = 0.5188 target = 0.241649 restraints weight = 4450.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.5194 r_free = 0.5194 target = 0.241039 restraints weight = 4527.783| |-----------------------------------------------------------------------------| r_work (final): 0.5001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5001 r_free = 0.5001 target_work(ls_wunit_k1) = 0.282 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5001 r_free = 0.5001 target_work(ls_wunit_k1) = 0.282 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.5001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5864 moved from start: 0.7019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 3531 Z= 0.180 Angle : 0.928 7.805 4830 Z= 0.453 Chirality : 0.069 0.465 606 Planarity : 0.003 0.029 579 Dihedral : 14.221 106.692 711 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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 aren not related in a simple way. whole: -4.02 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 180 TYR 0.016 0.002 TYR B 236 PHE 0.005 0.001 PHE C 171 HIS 0.002 0.002 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 3516) covalent geometry : angle 0.86331 ( 4788) SS BOND : bond 0.00905 ( 3) SS BOND : angle 1.83738 ( 6) hydrogen bonds : bond 0.06498 ( 66) hydrogen bonds : angle 6.19275 ( 198) link_NAG-ASN : bond 0.00428 ( 12) link_NAG-ASN : angle 3.98347 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.040 Fit side-chains REVERT: C 227 MET cc_start: 0.6492 (tpp) cc_final: 0.6281 (tpp) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0295 time to fit residues: 0.6074 Evaluate side-chains 11 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 34 optimal weight: 0.5980 chunk 37 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.5980 chunk 6 optimal weight: 0.0030 chunk 14 optimal weight: 9.9990 chunk 10 optimal weight: 0.0470 chunk 24 optimal weight: 5.9990 overall best weight: 0.3688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5125 r_free = 0.5125 target = 0.310768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.5182 r_free = 0.5182 target = 0.250015 restraints weight = 7802.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.5210 r_free = 0.5210 target = 0.246394 restraints weight = 5462.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.5214 r_free = 0.5214 target = 0.245799 restraints weight = 4431.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.5221 r_free = 0.5221 target = 0.245090 restraints weight = 3917.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.5227 r_free = 0.5227 target = 0.244174 restraints weight = 4300.893| |-----------------------------------------------------------------------------| r_work (final): 0.5042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5042 r_free = 0.5042 target_work(ls_wunit_k1) = 0.284 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5042 r_free = 0.5042 target_work(ls_wunit_k1) = 0.284 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.5042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5776 moved from start: 0.6942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 3531 Z= 0.168 Angle : 0.950 9.614 4830 Z= 0.470 Chirality : 0.082 0.817 606 Planarity : 0.003 0.024 579 Dihedral : 13.752 106.295 711 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.79 % Allowed : 0.00 % Favored : 99.21 % 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 aren not related in a simple way. whole: -4.03 (0.36), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 180 TYR 0.014 0.002 TYR B 236 PHE 0.005 0.001 PHE A 171 HIS 0.001 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 3516) covalent geometry : angle 0.89880 ( 4788) SS BOND : bond 0.00608 ( 3) SS BOND : angle 1.41425 ( 6) hydrogen bonds : bond 0.06281 ( 66) hydrogen bonds : angle 6.38868 ( 198) link_NAG-ASN : bond 0.00507 ( 12) link_NAG-ASN : angle 3.64756 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.025 Fit side-chains REVERT: C 206 GLU cc_start: 0.7934 (pm20) cc_final: 0.7593 (mm-30) REVERT: C 227 MET cc_start: 0.6205 (tpp) cc_final: 0.5989 (tpp) REVERT: C 239 HIS cc_start: 0.6845 (OUTLIER) cc_final: 0.6419 (m90) outliers start: 1 outliers final: 0 residues processed: 18 average time/residue: 0.0261 time to fit residues: 0.5959 Evaluate side-chains 14 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 0 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 25 optimal weight: 0.0270 chunk 17 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 4 optimal weight: 0.0470 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5122 r_free = 0.5122 target = 0.316096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.5194 r_free = 0.5194 target = 0.257829 restraints weight = 11994.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5203 r_free = 0.5203 target = 0.256047 restraints weight = 5515.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.5229 r_free = 0.5229 target = 0.253932 restraints weight = 4070.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.5233 r_free = 0.5233 target = 0.253494 restraints weight = 4315.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.5239 r_free = 0.5239 target = 0.252892 restraints weight = 3977.454| |-----------------------------------------------------------------------------| r_work (final): 0.5042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5042 r_free = 0.5042 target_work(ls_wunit_k1) = 0.293 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5042 r_free = 0.5042 target_work(ls_wunit_k1) = 0.293 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.5042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5685 moved from start: 0.6954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 3531 Z= 0.159 Angle : 0.874 8.595 4830 Z= 0.433 Chirality : 0.065 0.419 606 Planarity : 0.003 0.023 579 Dihedral : 13.223 104.370 711 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 aren not related in a simple way. whole: -3.91 (0.36), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 180 TYR 0.014 0.001 TYR B 248 PHE 0.005 0.001 PHE A 171 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 3516) covalent geometry : angle 0.82298 ( 4788) SS BOND : bond 0.00536 ( 3) SS BOND : angle 1.35636 ( 6) hydrogen bonds : bond 0.06100 ( 66) hydrogen bonds : angle 6.19712 ( 198) link_NAG-ASN : bond 0.00485 ( 12) link_NAG-ASN : angle 3.46780 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 671.00 seconds wall clock time: 12 minutes 19.76 seconds (739.76 seconds total)