Starting phenix.real_space_refine on Wed Jul 1 22:34:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7u14_26277/07_2026/7u14_26277.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u14_26277/07_2026/7u14_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_26277/07_2026/7u14_26277.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u14_26277/07_2026/7u14_26277.map" model { file = "/net/cci-nas-00/data/ceres_data/7u14_26277/07_2026/7u14_26277.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u14_26277/07_2026/7u14_26277.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7u14_26277/07_2026/7u14_26277.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7u14_26277/07_2026/7u14_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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 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 chiralities: 4 Time building chain proxies: 1.55, per 1000 atoms: 0.45 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 224.0 milliseconds 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: 0.10 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: 0.45 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 - 17.31: 1761 17.31 - 34.63: 177 34.63 - 51.94: 60 51.94 - 69.26: 15 69.26 - 86.57: 6 Dihedral angle restraints: 2019 sinusoidal: 786 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 2016 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: 1.440 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.960 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5170 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 : 16.903 86.572 1224 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 are 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/Z covalent geometry : bond 0.00637 / 0.29 ( 3516) covalent geometry : angle 0.94464 / 0.49 ( 4788) SS BOND : bond 0.00725 / 0.36 ( 3) SS BOND : angle 2.35437 / 1.27 ( 6) hydrogen bonds : bond 0.13721 / 9.82 ( 66) hydrogen bonds : angle 8.52990 / 5.70 ( 198) link_NAG-ASN : bond 0.00574 / 0.37 ( 12) link_NAG-ASN : angle 2.12511 / 1.34 ( 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 : 0.041 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: 0.4232 (OUTLIER) cc_final: 0.4021 (p0) outliers start: 8 outliers final: 0 residues processed: 25 average time/residue: 0.0375 time to fit residues: 1.1040 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 : 0.039 ------------------------------------------------------------------------------- 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... A 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 = 0.5300 r_free = 0.5300 target = 0.403642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5413 r_free = 0.5413 target = 0.344824 restraints weight = 15242.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.5441 r_free = 0.5441 target = 0.344706 restraints weight = 7921.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.5568 r_free = 0.5568 target = 0.341089 restraints weight = 5122.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.5569 r_free = 0.5569 target = 0.339698 restraints weight = 5421.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.5591 r_free = 0.5591 target = 0.339078 restraints weight = 4343.528| |-----------------------------------------------------------------------------| r_work (final): 0.5215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5216 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5216 r_free = 0.5216 target_work(ls_wunit_k1) = 0.324 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5223 r_free = 0.5223 target_work(ls_wunit_k1) = 0.324 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.5223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5310 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3531 Z= 0.170 Angle : 0.803 8.332 4830 Z= 0.417 Chirality : 0.070 0.524 606 Planarity : 0.003 0.020 579 Dihedral : 6.565 24.564 459 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 4.72 % 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 are not related in a simple way. whole: -3.39 (0.37), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 247 TYR 0.012 0.002 TYR C 143 PHE 0.009 0.002 PHE A 237 HIS 0.005 0.002 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 3516) covalent geometry : angle 0.77475 / 0.41 ( 4788) SS BOND : bond 0.00737 / 0.37 ( 3) SS BOND : angle 2.54537 / 1.37 ( 6) hydrogen bonds : bond 0.07872 / 5.65 ( 66) hydrogen bonds : angle 6.53819 / 4.33 ( 198) link_NAG-ASN : bond 0.00558 / 0.35 ( 12) link_NAG-ASN : angle 2.36316 / 1.52 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 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 16 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.051 Fit side-chains REVERT: C 207 MET cc_start: 0.3289 (ptm) cc_final: 0.2727 (tpt) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0299 time to fit residues: 0.6252 Evaluate side-chains 9 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.050 ------------------------------------------------------------------------------- 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: 2.9990 chunk 2 optimal weight: 0.1980 chunk 11 optimal weight: 7.9990 chunk 15 optimal weight: 0.0970 chunk 31 optimal weight: 0.7980 chunk 14 optimal weight: 0.0040 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 0.0970 chunk 22 optimal weight: 20.0000 chunk 20 optimal weight: 0.2980 overall best weight: 0.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.5276 r_free = 0.5276 target = 0.349525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5367 r_free = 0.5367 target = 0.295167 restraints weight = 12178.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5393 r_free = 0.5393 target = 0.293129 restraints weight = 6405.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.5445 r_free = 0.5445 target = 0.290575 restraints weight = 4270.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.5448 r_free = 0.5448 target = 0.289993 restraints weight = 4874.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.5449 r_free = 0.5449 target = 0.289958 restraints weight = 3811.395| |-----------------------------------------------------------------------------| r_work (final): 0.5206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5206 r_free = 0.5206 target_work(ls_wunit_k1) = 0.322 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5206 r_free = 0.5206 target_work(ls_wunit_k1) = 0.322 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.5206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5348 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3531 Z= 0.152 Angle : 0.836 9.792 4830 Z= 0.410 Chirality : 0.066 0.396 606 Planarity : 0.003 0.019 579 Dihedral : 6.032 23.206 459 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 1.57 % Allowed : 1.57 % 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 are not related in a simple way. whole: -3.26 (0.37), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 180 TYR 0.012 0.001 TYR A 143 PHE 0.011 0.002 PHE B 237 HIS 0.006 0.003 HIS B 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 3516) covalent geometry : angle 0.76068 / 0.39 ( 4788) SS BOND : bond 0.00728 / 0.36 ( 3) SS BOND : angle 2.06202 / 1.11 ( 6) hydrogen bonds : bond 0.07204 / 5.08 ( 66) hydrogen bonds : angle 6.40186 / 4.21 ( 198) link_NAG-ASN : bond 0.00740 / 0.48 ( 12) link_NAG-ASN : angle 4.00420 / 2.62 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 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 21 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.043 Fit side-chains REVERT: C 140 ARG cc_start: 0.7334 (tpt90) cc_final: 0.5776 (tmt170) REVERT: C 222 HIS cc_start: 0.6699 (OUTLIER) cc_final: 0.5694 (p90) outliers start: 2 outliers final: 0 residues processed: 20 average time/residue: 0.0465 time to fit residues: 1.0886 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 : 0.043 ------------------------------------------------------------------------------- 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: 0.0060 chunk 34 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 30 optimal weight: 0.0020 chunk 27 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 overall best weight: 2.1808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5224 r_free = 0.5224 target = 0.370588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.5322 r_free = 0.5322 target = 0.319642 restraints weight = 5117.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5349 r_free = 0.5349 target = 0.317291 restraints weight = 4712.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5349 r_free = 0.5349 target = 0.317291 restraints weight = 3442.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5349 r_free = 0.5349 target = 0.317291 restraints weight = 3348.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5349 r_free = 0.5349 target = 0.317291 restraints weight = 3348.774| |-----------------------------------------------------------------------------| r_work (final): 0.5175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5175 r_free = 0.5175 target_work(ls_wunit_k1) = 0.347 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5175 r_free = 0.5175 target_work(ls_wunit_k1) = 0.347 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.5175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5560 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3531 Z= 0.148 Angle : 0.849 9.566 4830 Z= 0.421 Chirality : 0.071 0.599 606 Planarity : 0.003 0.016 579 Dihedral : 6.261 24.305 459 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.79 % Allowed : 0.79 % 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 are not related in a simple way. whole: -3.24 (0.38), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 247 TYR 0.012 0.002 TYR A 143 PHE 0.008 0.002 PHE B 237 HIS 0.001 0.001 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 3516) covalent geometry : angle 0.79006 / 0.41 ( 4788) SS BOND : bond 0.00507 / 0.25 ( 3) SS BOND : angle 2.04182 / 1.10 ( 6) hydrogen bonds : bond 0.06467 / 4.55 ( 66) hydrogen bonds : angle 6.06373 / 4.00 ( 198) link_NAG-ASN : bond 0.00718 / 0.47 ( 12) link_NAG-ASN : angle 3.59616 / 2.35 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 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 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 Fit side-chains REVERT: C 140 ARG cc_start: 0.7329 (tpt90) cc_final: 0.5687 (tmt170) REVERT: C 207 MET cc_start: 0.2340 (ptm) cc_final: 0.2079 (tpt) REVERT: C 229 GLN cc_start: 0.7116 (tt0) cc_final: 0.5621 (mp10) outliers start: 1 outliers final: 0 residues processed: 18 average time/residue: 0.0488 time to fit residues: 1.0210 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 : 0.041 ------------------------------------------------------------------------------- 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: 6.9990 chunk 24 optimal weight: 4.9990 chunk 7 optimal weight: 0.2980 chunk 37 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 9 optimal weight: 20.0000 chunk 27 optimal weight: 0.1980 chunk 16 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 242 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 = 0.5213 r_free = 0.5213 target = 0.339113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.5301 r_free = 0.5301 target = 0.287511 restraints weight = 7912.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.5304 r_free = 0.5304 target = 0.287283 restraints weight = 6123.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.5328 r_free = 0.5328 target = 0.286359 restraints weight = 4915.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.5328 r_free = 0.5328 target = 0.286315 restraints weight = 4502.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5329 r_free = 0.5329 target = 0.286293 restraints weight = 4124.576| |-----------------------------------------------------------------------------| r_work (final): 0.5148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5147 r_free = 0.5147 target_work(ls_wunit_k1) = 0.317 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5147 r_free = 0.5147 target_work(ls_wunit_k1) = 0.317 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.5147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5545 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3531 Z= 0.157 Angle : 0.806 7.946 4830 Z= 0.407 Chirality : 0.065 0.329 606 Planarity : 0.003 0.013 579 Dihedral : 6.196 24.534 459 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 15.24 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 are not related in a simple way. whole: -3.33 (0.38), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 247 TYR 0.011 0.001 TYR B 143 PHE 0.008 0.001 PHE C 237 HIS 0.001 0.001 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 ( 3516) covalent geometry : angle 0.75383 / 0.40 ( 4788) SS BOND : bond 0.00552 / 0.28 ( 3) SS BOND : angle 1.72562 / 0.93 ( 6) hydrogen bonds : bond 0.06279 / 4.46 ( 66) hydrogen bonds : angle 6.01074 / 3.98 ( 198) link_NAG-ASN : bond 0.00694 / 0.45 ( 12) link_NAG-ASN : angle 3.32563 / 2.16 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 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 17 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.042 Fit side-chains REVERT: C 140 ARG cc_start: 0.7349 (tpt90) cc_final: 0.5632 (tmt170) REVERT: C 228 MET cc_start: 0.4447 (ptp) cc_final: 0.4106 (ppp) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0490 time to fit residues: 0.9724 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 : 0.041 ------------------------------------------------------------------------------- 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: 20.0000 chunk 3 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5200 r_free = 0.5200 target = 0.356881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5296 r_free = 0.5296 target = 0.300029 restraints weight = 5221.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.5336 r_free = 0.5336 target = 0.294211 restraints weight = 4967.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.5339 r_free = 0.5339 target = 0.293707 restraints weight = 3752.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.5342 r_free = 0.5342 target = 0.293318 restraints weight = 3501.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.5345 r_free = 0.5345 target = 0.293134 restraints weight = 3078.068| |-----------------------------------------------------------------------------| r_work (final): 0.5132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5133 r_free = 0.5133 target_work(ls_wunit_k1) = 0.332 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5133 r_free = 0.5133 target_work(ls_wunit_k1) = 0.332 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.5133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5778 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3531 Z= 0.168 Angle : 0.833 7.341 4830 Z= 0.420 Chirality : 0.064 0.336 606 Planarity : 0.003 0.015 579 Dihedral : 6.444 26.276 459 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % 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 are not related in a simple way. whole: -3.37 (0.37), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 180 TYR 0.014 0.002 TYR B 143 PHE 0.006 0.001 PHE A 237 HIS 0.001 0.001 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.17 ( 3516) covalent geometry : angle 0.77559 / 0.41 ( 4788) SS BOND : bond 0.00506 / 0.25 ( 3) SS BOND : angle 2.05442 / 1.11 ( 6) hydrogen bonds : bond 0.06432 / 4.55 ( 66) hydrogen bonds : angle 5.74393 / 3.79 ( 198) link_NAG-ASN : bond 0.00684 / 0.44 ( 12) link_NAG-ASN : angle 3.50408 / 2.27 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 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 17 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.045 Fit side-chains REVERT: C 206 GLU cc_start: 0.7595 (pm20) cc_final: 0.7031 (mm-30) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0179 time to fit residues: 0.4003 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 : 0.026 ------------------------------------------------------------------------------- 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: 10.0000 chunk 17 optimal weight: 9.9990 chunk 14 optimal weight: 0.0370 chunk 25 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 3 optimal weight: 0.2980 chunk 6 optimal weight: 20.0000 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 10 optimal weight: 40.0000 overall best weight: 2.8664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 229 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 = 0.5210 r_free = 0.5210 target = 0.353720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.5292 r_free = 0.5292 target = 0.296798 restraints weight = 5707.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5310 r_free = 0.5310 target = 0.293462 restraints weight = 5223.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.5331 r_free = 0.5331 target = 0.290297 restraints weight = 3288.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.5331 r_free = 0.5331 target = 0.290287 restraints weight = 2970.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.5367 r_free = 0.5367 target = 0.287264 restraints weight = 3045.993| |-----------------------------------------------------------------------------| r_work (final): 0.5139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5139 r_free = 0.5139 target_work(ls_wunit_k1) = 0.328 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5139 r_free = 0.5139 target_work(ls_wunit_k1) = 0.328 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.5139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5807 moved from start: 0.5698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 3531 Z= 0.170 Angle : 0.852 7.354 4830 Z= 0.422 Chirality : 0.070 0.402 606 Planarity : 0.003 0.014 579 Dihedral : 6.606 26.947 459 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % 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 are not related in a simple way. whole: -3.40 (0.38), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 247 TYR 0.013 0.002 TYR B 236 PHE 0.009 0.002 PHE C 237 HIS 0.003 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.17 ( 3516) covalent geometry : angle 0.79149 / 0.41 ( 4788) SS BOND : bond 0.00768 / 0.39 ( 3) SS BOND : angle 2.16200 / 1.17 ( 6) hydrogen bonds : bond 0.06384 / 4.54 ( 66) hydrogen bonds : angle 5.66103 / 3.78 ( 198) link_NAG-ASN : bond 0.00634 / 0.41 ( 12) link_NAG-ASN : angle 3.65199 / 2.34 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 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 15 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.050 Fit side-chains REVERT: C 206 GLU cc_start: 0.7722 (pm20) cc_final: 0.7027 (mm-30) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0290 time to fit residues: 0.5717 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 : 0.041 ------------------------------------------------------------------------------- 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: 0.7980 chunk 8 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 0.0970 chunk 4 optimal weight: 0.1980 chunk 26 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.5244 r_free = 0.5244 target = 0.362114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.5343 r_free = 0.5343 target = 0.302276 restraints weight = 5802.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.5363 r_free = 0.5363 target = 0.299812 restraints weight = 5215.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.5384 r_free = 0.5384 target = 0.297452 restraints weight = 3854.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5384 r_free = 0.5384 target = 0.297381 restraints weight = 3305.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.5385 r_free = 0.5385 target = 0.297333 restraints weight = 3371.240| |-----------------------------------------------------------------------------| r_work (final): 0.5156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5156 r_free = 0.5156 target_work(ls_wunit_k1) = 0.336 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5156 r_free = 0.5156 target_work(ls_wunit_k1) = 0.336 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.5156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5741 moved from start: 0.5850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 3531 Z= 0.185 Angle : 0.883 7.707 4830 Z= 0.436 Chirality : 0.086 0.745 606 Planarity : 0.003 0.011 579 Dihedral : 6.550 27.051 459 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % 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 are not related in a simple way. whole: -3.40 (0.39), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 180 TYR 0.014 0.002 TYR B 236 PHE 0.009 0.001 PHE A 237 HIS 0.001 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.18 ( 3516) covalent geometry : angle 0.83076 / 0.43 ( 4788) SS BOND : bond 0.00641 / 0.32 ( 3) SS BOND : angle 1.67745 / 0.90 ( 6) hydrogen bonds : bond 0.06075 / 4.31 ( 66) hydrogen bonds : angle 5.91600 / 3.94 ( 198) link_NAG-ASN : bond 0.00482 / 0.33 ( 12) link_NAG-ASN : angle 3.52413 / 2.26 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 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 13 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.025 Fit side-chains REVERT: C 206 GLU cc_start: 0.7732 (pm20) cc_final: 0.7141 (mm-30) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0174 time to fit residues: 0.3090 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 : 0.025 ------------------------------------------------------------------------------- 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: 6.9990 chunk 20 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 32 optimal weight: 0.0470 chunk 6 optimal weight: 0.0170 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 overall best weight: 2.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.5235 r_free = 0.5235 target = 0.360656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.5295 r_free = 0.5295 target = 0.308623 restraints weight = 5356.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.5323 r_free = 0.5323 target = 0.303906 restraints weight = 4904.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5328 r_free = 0.5328 target = 0.302964 restraints weight = 3849.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5328 r_free = 0.5328 target = 0.302964 restraints weight = 3331.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5328 r_free = 0.5328 target = 0.302964 restraints weight = 3331.569| |-----------------------------------------------------------------------------| r_work (final): 0.5138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5138 r_free = 0.5138 target_work(ls_wunit_k1) = 0.338 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5138 r_free = 0.5138 target_work(ls_wunit_k1) = 0.338 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.5138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5790 moved from start: 0.6184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 3531 Z= 0.184 Angle : 0.940 10.878 4830 Z= 0.460 Chirality : 0.087 0.799 606 Planarity : 0.003 0.014 579 Dihedral : 6.751 28.001 459 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % 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 are not related in a simple way. whole: -3.48 (0.38), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 180 TYR 0.013 0.002 TYR B 143 PHE 0.009 0.002 PHE C 237 HIS 0.001 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.18 ( 3516) covalent geometry : angle 0.89195 / 0.45 ( 4788) SS BOND : bond 0.00828 / 0.42 ( 3) SS BOND : angle 2.12920 / 1.15 ( 6) hydrogen bonds : bond 0.06280 / 4.44 ( 66) hydrogen bonds : angle 6.09279 / 4.09 ( 198) link_NAG-ASN : bond 0.00507 / 0.34 ( 12) link_NAG-ASN : angle 3.44915 / 2.19 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 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 14 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.051 Fit side-chains REVERT: C 206 GLU cc_start: 0.7687 (pm20) cc_final: 0.7112 (mm-30) REVERT: C 227 MET cc_start: 0.5339 (mmm) cc_final: 0.3480 (pmm) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0293 time to fit residues: 0.5538 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 : 0.052 ------------------------------------------------------------------------------- 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: 0.0470 chunk 37 optimal weight: 7.9990 chunk 23 optimal weight: 30.0000 chunk 1 optimal weight: 10.0000 chunk 8 optimal weight: 0.1980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.1980 chunk 6 optimal weight: 0.4980 chunk 14 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 overall best weight: 1.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5265 r_free = 0.5265 target = 0.365455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5367 r_free = 0.5367 target = 0.310506 restraints weight = 7562.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.5372 r_free = 0.5372 target = 0.309165 restraints weight = 5533.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5372 r_free = 0.5372 target = 0.309165 restraints weight = 4441.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5372 r_free = 0.5372 target = 0.309165 restraints weight = 4437.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5372 r_free = 0.5372 target = 0.309165 restraints weight = 4436.927| |-----------------------------------------------------------------------------| r_work (final): 0.5176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5176 r_free = 0.5176 target_work(ls_wunit_k1) = 0.344 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5176 r_free = 0.5176 target_work(ls_wunit_k1) = 0.344 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.5176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5740 moved from start: 0.6218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 3531 Z= 0.180 Angle : 0.869 7.554 4830 Z= 0.428 Chirality : 0.069 0.395 606 Planarity : 0.002 0.012 579 Dihedral : 6.628 27.899 459 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 18.61 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 are not related in a simple way. whole: -3.47 (0.37), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 247 TYR 0.011 0.001 TYR C 143 PHE 0.010 0.002 PHE C 237 HIS 0.001 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.18 ( 3516) covalent geometry : angle 0.82388 / 0.42 ( 4788) SS BOND : bond 0.00580 / 0.29 ( 3) SS BOND : angle 1.55879 / 0.84 ( 6) hydrogen bonds : bond 0.06117 / 4.36 ( 66) hydrogen bonds : angle 5.82104 / 3.91 ( 198) link_NAG-ASN : bond 0.00506 / 0.34 ( 12) link_NAG-ASN : angle 3.27155 / 2.07 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 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 13 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.025 Fit side-chains REVERT: C 206 GLU cc_start: 0.7621 (pm20) cc_final: 0.7048 (mm-30) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0172 time to fit residues: 0.3013 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 : 0.025 ------------------------------------------------------------------------------- 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: 7.9990 chunk 33 optimal weight: 0.4980 chunk 25 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.5274 r_free = 0.5274 target = 0.413178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.5278 r_free = 0.5278 target = 0.357774 restraints weight = 14646.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.5418 r_free = 0.5418 target = 0.331067 restraints weight = 3498.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.5437 r_free = 0.5437 target = 0.326975 restraints weight = 3691.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.5438 r_free = 0.5438 target = 0.326903 restraints weight = 4293.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5438 r_free = 0.5438 target = 0.326900 restraints weight = 3238.999| |-----------------------------------------------------------------------------| r_work (final): 0.5100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5100 r_free = 0.5100 target_work(ls_wunit_k1) = 0.323 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5100 r_free = 0.5100 target_work(ls_wunit_k1) = 0.323 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.5100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5898 moved from start: 0.6456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 3531 Z= 0.183 Angle : 0.919 7.832 4830 Z= 0.463 Chirality : 0.071 0.447 606 Planarity : 0.003 0.015 579 Dihedral : 6.946 28.508 459 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % 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 are not related in a simple way. whole: -3.50 (0.37), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 247 TYR 0.015 0.002 TYR B 143 PHE 0.011 0.002 PHE C 237 HIS 0.002 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.18 ( 3516) covalent geometry : angle 0.86670 / 0.45 ( 4788) SS BOND : bond 0.00903 / 0.45 ( 3) SS BOND : angle 2.21525 / 1.19 ( 6) hydrogen bonds : bond 0.06452 / 4.64 ( 66) hydrogen bonds : angle 5.53991 / 3.73 ( 198) link_NAG-ASN : bond 0.00472 / 0.32 ( 12) link_NAG-ASN : angle 3.54007 / 2.23 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 719.53 seconds wall clock time: 13 minutes 8.94 seconds (788.94 seconds total)