Starting phenix.real_space_refine on Mon Apr 6 10:02:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qgu_53148/04_2026/9qgu_53148_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qgu_53148/04_2026/9qgu_53148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qgu_53148/04_2026/9qgu_53148_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qgu_53148/04_2026/9qgu_53148_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qgu_53148/04_2026/9qgu_53148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qgu_53148/04_2026/9qgu_53148.map" } resolution = 3.69 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= 0.001 sd= 0.031 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 32 5.16 5 C 5558 2.51 5 N 1456 2.21 5 O 1518 1.98 5 H 8566 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17134 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 4441 Classifications: {'peptide': 265} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 252} Chain: "B" Number of atoms: 4441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 4441 Classifications: {'peptide': 265} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 252} Chain: "C" Number of atoms: 4030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 4030 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 255} Chain: "D" Number of atoms: 4030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 4030 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 255} Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'AV0': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'AV0': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.77, per 1000 atoms: 0.16 Number of scatterers: 17134 At special positions: 0 Unit cell: (81.9, 105.3, 109.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 32 16.00 P 4 15.00 O 1518 8.00 N 1456 7.00 C 5558 6.00 H 8566 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 613.0 milliseconds 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 4 sheets defined 68.1% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 32 through 45 removed outlier: 4.030A pdb=" N ALA A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 65 removed outlier: 3.587A pdb=" N SER A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 87 removed outlier: 4.134A pdb=" N ILE A 72 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 75 " --> pdb=" O TRP A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 94 through 120 Proline residue: A 100 - end of helix Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 126 through 131 removed outlier: 3.924A pdb=" N LYS A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 166 removed outlier: 4.220A pdb=" N HIS A 140 " --> pdb=" O PRO A 136 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE A 158 " --> pdb=" O HIS A 154 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.897A pdb=" N LEU A 175 " --> pdb=" O PHE A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 200 removed outlier: 3.923A pdb=" N TRP A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 219 removed outlier: 3.537A pdb=" N LEU A 208 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 229 removed outlier: 3.748A pdb=" N MET A 228 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 241 removed outlier: 3.662A pdb=" N VAL A 239 " --> pdb=" O LYS A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 258 removed outlier: 4.023A pdb=" N HIS A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 262 through 288 removed outlier: 4.216A pdb=" N TRP A 266 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG A 288 " --> pdb=" O MET A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'B' and resid 32 through 45 removed outlier: 4.030A pdb=" N ALA B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 65 removed outlier: 3.587A pdb=" N SER B 65 " --> pdb=" O ARG B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 87 removed outlier: 4.134A pdb=" N ILE B 72 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 75 " --> pdb=" O TRP B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 94 through 120 Proline residue: B 100 - end of helix Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 126 through 131 removed outlier: 3.923A pdb=" N LYS B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 166 removed outlier: 4.219A pdb=" N HIS B 140 " --> pdb=" O PRO B 136 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE B 158 " --> pdb=" O HIS B 154 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 162 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 175 removed outlier: 3.897A pdb=" N LEU B 175 " --> pdb=" O PHE B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 200 removed outlier: 3.923A pdb=" N TRP B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 219 removed outlier: 3.537A pdb=" N LEU B 208 " --> pdb=" O ASP B 204 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 removed outlier: 3.749A pdb=" N MET B 228 " --> pdb=" O ASN B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 241 removed outlier: 3.662A pdb=" N VAL B 239 " --> pdb=" O LYS B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 258 removed outlier: 4.023A pdb=" N HIS B 247 " --> pdb=" O ASN B 243 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE B 252 " --> pdb=" O PHE B 248 " (cutoff:3.500A) Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 262 through 288 removed outlier: 4.216A pdb=" N TRP B 266 " --> pdb=" O GLN B 262 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG B 288 " --> pdb=" O MET B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 295 Processing helix chain 'C' and resid 22 through 32 Processing helix chain 'C' and resid 70 through 79 removed outlier: 3.692A pdb=" N LEU C 74 " --> pdb=" O GLY C 70 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 75 " --> pdb=" O LYS C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 113 through 122 removed outlier: 4.071A pdb=" N GLY C 119 " --> pdb=" O ILE C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 134 Processing helix chain 'C' and resid 136 through 142 Processing helix chain 'C' and resid 156 through 167 removed outlier: 3.869A pdb=" N GLY C 164 " --> pdb=" O ARG C 160 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR C 167 " --> pdb=" O MET C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 183 Processing helix chain 'C' and resid 184 through 202 removed outlier: 5.319A pdb=" N ILE C 193 " --> pdb=" O LYS C 189 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ARG C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 219 Processing helix chain 'C' and resid 236 through 263 removed outlier: 6.841A pdb=" N ASP C 246 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N GLU C 247 " --> pdb=" O TYR C 243 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ALA C 248 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 32 Processing helix chain 'D' and resid 70 through 79 removed outlier: 3.692A pdb=" N LEU D 74 " --> pdb=" O GLY D 70 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D 75 " --> pdb=" O LYS D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 112 No H-bonds generated for 'chain 'D' and resid 110 through 112' Processing helix chain 'D' and resid 113 through 122 removed outlier: 4.071A pdb=" N GLY D 119 " --> pdb=" O ILE D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 134 Processing helix chain 'D' and resid 136 through 142 Processing helix chain 'D' and resid 156 through 167 removed outlier: 3.870A pdb=" N GLY D 164 " --> pdb=" O ARG D 160 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR D 167 " --> pdb=" O MET D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 183 Processing helix chain 'D' and resid 184 through 202 removed outlier: 5.319A pdb=" N ILE D 193 " --> pdb=" O LYS D 189 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 219 Processing helix chain 'D' and resid 236 through 263 removed outlier: 6.841A pdb=" N ASP D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N GLU D 247 " --> pdb=" O TYR D 243 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA D 248 " --> pdb=" O GLU D 244 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 51 through 54 removed outlier: 7.547A pdb=" N LEU C 53 " --> pdb=" O HIS C 7 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N HIS C 7 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA C 9 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG C 86 " --> pdb=" O ALA C 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 95 through 98 removed outlier: 3.821A pdb=" N LEU C 175 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU C 174 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ALA C 208 " --> pdb=" O LEU C 174 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU C 176 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL C 61 " --> pdb=" O PHE C 207 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ARG C 60 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N MET C 223 " --> pdb=" O ARG C 60 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLY C 62 " --> pdb=" O MET C 223 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ILE C 225 " --> pdb=" O GLY C 62 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL C 64 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ALA C 222 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N SER C 233 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N TRP C 224 " --> pdb=" O LYS C 231 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 51 through 54 removed outlier: 7.547A pdb=" N LEU D 53 " --> pdb=" O HIS D 7 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N HIS D 7 " --> pdb=" O LEU D 53 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA D 9 " --> pdb=" O ARG D 86 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG D 86 " --> pdb=" O ALA D 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 95 through 98 removed outlier: 3.821A pdb=" N LEU D 175 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU D 174 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ALA D 208 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU D 176 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL D 61 " --> pdb=" O PHE D 207 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ARG D 60 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N MET D 223 " --> pdb=" O ARG D 60 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLY D 62 " --> pdb=" O MET D 223 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ILE D 225 " --> pdb=" O GLY D 62 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL D 64 " --> pdb=" O ILE D 225 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ALA D 222 " --> pdb=" O SER D 233 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N SER D 233 " --> pdb=" O ALA D 222 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N TRP D 224 " --> pdb=" O LYS D 231 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1326 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: 3.02 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8562 1.03 - 1.23: 20 1.23 - 1.43: 3646 1.43 - 1.62: 5050 1.62 - 1.82: 60 Bond restraints: 17338 Sorted by residual: bond pdb=" CA ASN B 187 " pdb=" HA ASN B 187 " ideal model delta sigma weight residual 0.970 0.917 0.053 2.00e-02 2.50e+03 6.96e+00 bond pdb=" CA ASN A 187 " pdb=" HA ASN A 187 " ideal model delta sigma weight residual 0.970 0.918 0.052 2.00e-02 2.50e+03 6.79e+00 bond pdb=" C MET B 219 " pdb=" N THR B 220 " ideal model delta sigma weight residual 1.327 1.355 -0.028 1.71e-02 3.42e+03 2.76e+00 bond pdb=" C MET A 219 " pdb=" N THR A 220 " ideal model delta sigma weight residual 1.327 1.355 -0.028 1.71e-02 3.42e+03 2.71e+00 bond pdb=" CB PHE D 187 " pdb=" CG PHE D 187 " ideal model delta sigma weight residual 1.502 1.536 -0.034 2.30e-02 1.89e+03 2.13e+00 ... (remaining 17333 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.98: 31196 3.98 - 7.96: 114 7.96 - 11.93: 2 11.93 - 15.91: 0 15.91 - 19.89: 2 Bond angle restraints: 31314 Sorted by residual: angle pdb=" N ASN B 187 " pdb=" CA ASN B 187 " pdb=" HA ASN B 187 " ideal model delta sigma weight residual 110.00 90.11 19.89 3.00e+00 1.11e-01 4.40e+01 angle pdb=" N ASN A 187 " pdb=" CA ASN A 187 " pdb=" HA ASN A 187 " ideal model delta sigma weight residual 110.00 90.17 19.83 3.00e+00 1.11e-01 4.37e+01 angle pdb=" C ASN B 187 " pdb=" CA ASN B 187 " pdb=" HA ASN B 187 " ideal model delta sigma weight residual 109.00 120.22 -11.22 3.00e+00 1.11e-01 1.40e+01 angle pdb=" C ASN A 187 " pdb=" CA ASN A 187 " pdb=" HA ASN A 187 " ideal model delta sigma weight residual 109.00 120.19 -11.19 3.00e+00 1.11e-01 1.39e+01 angle pdb=" CA TRP B 50 " pdb=" CB TRP B 50 " pdb=" CG TRP B 50 " ideal model delta sigma weight residual 113.60 119.70 -6.10 1.90e+00 2.77e-01 1.03e+01 ... (remaining 31309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.14: 7461 21.14 - 42.28: 560 42.28 - 63.42: 161 63.42 - 84.56: 26 84.56 - 105.70: 12 Dihedral angle restraints: 8220 sinusoidal: 4590 harmonic: 3630 Sorted by residual: dihedral pdb=" C5' ADP C 301 " pdb=" O5' ADP C 301 " pdb=" PA ADP C 301 " pdb=" O2A ADP C 301 " ideal model delta sinusoidal sigma weight residual -60.00 -144.99 85.00 1 2.00e+01 2.50e-03 2.19e+01 dihedral pdb=" C5' ADP D 301 " pdb=" O5' ADP D 301 " pdb=" PA ADP D 301 " pdb=" O2A ADP D 301 " ideal model delta sinusoidal sigma weight residual -60.00 -144.97 84.97 1 2.00e+01 2.50e-03 2.19e+01 dihedral pdb=" CBQ AV0 B 301 " pdb=" CBS AV0 B 301 " pdb=" CCM AV0 B 301 " pdb=" O1 AV0 B 301 " ideal model delta sinusoidal sigma weight residual 70.26 175.96 -105.70 1 3.00e+01 1.11e-03 1.36e+01 ... (remaining 8217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1280 0.081 - 0.162: 100 0.162 - 0.243: 2 0.243 - 0.324: 0 0.324 - 0.405: 2 Chirality restraints: 1384 Sorted by residual: chirality pdb=" CCS AV0 A 301 " pdb=" CCW AV0 A 301 " pdb=" OBZ AV0 A 301 " pdb=" OCB AV0 A 301 " both_signs ideal model delta sigma weight residual False 2.24 1.83 0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CCS AV0 B 301 " pdb=" CCW AV0 B 301 " pdb=" OBZ AV0 B 301 " pdb=" OCB AV0 B 301 " both_signs ideal model delta sigma weight residual False 2.24 1.84 0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" CB VAL D 166 " pdb=" CA VAL D 166 " pdb=" CG1 VAL D 166 " pdb=" CG2 VAL D 166 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1381 not shown) Planarity restraints: 2474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 187 " 0.010 2.00e-02 2.50e+03 1.33e-02 5.27e+00 pdb=" CG PHE D 187 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE D 187 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE D 187 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE D 187 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE D 187 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE D 187 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE D 187 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE D 187 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE D 187 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE D 187 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE D 187 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 187 " -0.010 2.00e-02 2.50e+03 1.31e-02 5.15e+00 pdb=" CG PHE C 187 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE C 187 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE C 187 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE C 187 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 187 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE C 187 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE C 187 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE C 187 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE C 187 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE C 187 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE C 187 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 143 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C ARG B 143 " -0.033 2.00e-02 2.50e+03 pdb=" O ARG B 143 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU B 144 " 0.011 2.00e-02 2.50e+03 ... (remaining 2471 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 832 2.20 - 2.80: 34836 2.80 - 3.40: 47146 3.40 - 4.00: 59077 4.00 - 4.60: 92331 Nonbonded interactions: 234222 Sorted by model distance: nonbonded pdb=" HA ASN A 187 " pdb=" HE1 TRP A 190 " model vdw 1.601 2.270 nonbonded pdb=" HA ASN B 187 " pdb=" HE1 TRP B 190 " model vdw 1.601 2.270 nonbonded pdb=" HG SER B 65 " pdb=" H GLY B 68 " model vdw 1.717 2.100 nonbonded pdb=" O GLN B 52 " pdb="HE21 GLN B 52 " model vdw 1.828 2.450 nonbonded pdb=" O GLN A 52 " pdb="HE21 GLN A 52 " model vdw 1.829 2.450 ... (remaining 234217 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 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: 0.100 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.910 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.010 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8772 Z= 0.194 Angle : 0.871 7.466 11928 Z= 0.443 Chirality : 0.045 0.405 1384 Planarity : 0.006 0.043 1460 Dihedral : 17.021 105.697 3360 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 14.35 % Favored : 85.65 % 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: -1.96 (0.24), residues: 1046 helix: -0.94 (0.19), residues: 636 sheet: -1.08 (0.49), residues: 68 loop : -1.77 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 192 TYR 0.016 0.002 TYR A 166 PHE 0.036 0.002 PHE D 187 TRP 0.013 0.002 TRP B 71 HIS 0.014 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 8772) covalent geometry : angle 0.87065 (11928) hydrogen bonds : bond 0.16191 ( 458) hydrogen bonds : angle 7.89685 ( 1326) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 209 SER cc_start: 0.8503 (t) cc_final: 0.8146 (t) REVERT: D 209 SER cc_start: 0.8596 (t) cc_final: 0.8265 (t) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2080 time to fit residues: 45.3633 Evaluate side-chains 141 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN B 126 ASN C 67 ASN D 67 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.231665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.183332 restraints weight = 31245.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.189417 restraints weight = 15873.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.193084 restraints weight = 10807.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.194823 restraints weight = 8767.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.196021 restraints weight = 7901.308| |-----------------------------------------------------------------------------| r_work (final): 0.4295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8772 Z= 0.143 Angle : 0.638 6.386 11928 Z= 0.313 Chirality : 0.041 0.370 1384 Planarity : 0.004 0.042 1460 Dihedral : 11.126 111.774 1422 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.24 % Allowed : 13.79 % Favored : 83.97 % 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: -0.91 (0.25), residues: 1046 helix: -0.14 (0.20), residues: 642 sheet: -0.74 (0.53), residues: 68 loop : -1.25 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 253 TYR 0.009 0.001 TYR C 112 PHE 0.009 0.001 PHE C 207 TRP 0.011 0.001 TRP A 50 HIS 0.005 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8772) covalent geometry : angle 0.63846 (11928) hydrogen bonds : bond 0.04181 ( 458) hydrogen bonds : angle 4.79624 ( 1326) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6677 (tt) REVERT: C 67 ASN cc_start: 0.7422 (t0) cc_final: 0.7011 (t0) REVERT: C 112 TYR cc_start: 0.7636 (OUTLIER) cc_final: 0.5952 (t80) REVERT: D 23 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6717 (tt) REVERT: D 67 ASN cc_start: 0.7437 (t0) cc_final: 0.7017 (t0) REVERT: D 112 TYR cc_start: 0.7714 (OUTLIER) cc_final: 0.5983 (t80) REVERT: D 209 SER cc_start: 0.8727 (t) cc_final: 0.8517 (t) outliers start: 20 outliers final: 13 residues processed: 150 average time/residue: 0.2092 time to fit residues: 42.6252 Evaluate side-chains 159 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 207 PHE Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 229 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 77 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN B 148 GLN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.211618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.169337 restraints weight = 31278.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.171515 restraints weight = 25255.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.172937 restraints weight = 17607.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.173166 restraints weight = 15343.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.173320 restraints weight = 12935.613| |-----------------------------------------------------------------------------| r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8772 Z= 0.276 Angle : 0.731 8.356 11928 Z= 0.372 Chirality : 0.045 0.369 1384 Planarity : 0.004 0.047 1460 Dihedral : 12.888 135.461 1422 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.25 % Allowed : 14.91 % Favored : 81.84 % 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: -1.45 (0.25), residues: 1046 helix: -0.56 (0.19), residues: 636 sheet: -1.29 (0.54), residues: 68 loop : -1.39 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 94 TYR 0.017 0.002 TYR A 142 PHE 0.015 0.002 PHE A 248 TRP 0.012 0.002 TRP B 37 HIS 0.008 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00649 ( 8772) covalent geometry : angle 0.73104 (11928) hydrogen bonds : bond 0.04654 ( 458) hydrogen bonds : angle 4.96832 ( 1326) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 LEU cc_start: 0.8516 (tp) cc_final: 0.7769 (tt) REVERT: C 23 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6694 (tt) REVERT: C 112 TYR cc_start: 0.7768 (OUTLIER) cc_final: 0.6005 (t80) REVERT: D 23 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6901 (tt) REVERT: D 112 TYR cc_start: 0.7782 (OUTLIER) cc_final: 0.6006 (t80) outliers start: 29 outliers final: 15 residues processed: 152 average time/residue: 0.2160 time to fit residues: 44.7099 Evaluate side-chains 154 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 207 PHE Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 229 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 77 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 103 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.216979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.175822 restraints weight = 31012.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.175930 restraints weight = 20243.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.176856 restraints weight = 16247.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.177658 restraints weight = 13410.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.177982 restraints weight = 13268.562| |-----------------------------------------------------------------------------| r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8772 Z= 0.118 Angle : 0.585 7.012 11928 Z= 0.283 Chirality : 0.040 0.369 1384 Planarity : 0.003 0.044 1460 Dihedral : 11.685 140.155 1422 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.13 % Allowed : 15.47 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.26), residues: 1046 helix: -0.15 (0.20), residues: 646 sheet: -1.34 (0.56), residues: 68 loop : -1.20 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 192 TYR 0.007 0.001 TYR A 101 PHE 0.010 0.001 PHE C 207 TRP 0.010 0.001 TRP A 50 HIS 0.005 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8772) covalent geometry : angle 0.58477 (11928) hydrogen bonds : bond 0.03450 ( 458) hydrogen bonds : angle 4.46866 ( 1326) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 VAL cc_start: 0.7529 (t) cc_final: 0.7321 (p) REVERT: C 23 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6780 (tt) REVERT: C 112 TYR cc_start: 0.7717 (OUTLIER) cc_final: 0.5869 (t80) REVERT: D 23 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6892 (tt) REVERT: D 112 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.6033 (t80) outliers start: 19 outliers final: 10 residues processed: 159 average time/residue: 0.2203 time to fit residues: 47.7258 Evaluate side-chains 147 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 153 TYR Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 207 PHE Chi-restraints excluded: chain D residue 229 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 33 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 24 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 65 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.227238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.176701 restraints weight = 31475.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.182519 restraints weight = 16370.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.186141 restraints weight = 11330.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.187838 restraints weight = 9282.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.188523 restraints weight = 8376.658| |-----------------------------------------------------------------------------| r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8772 Z= 0.114 Angle : 0.574 6.444 11928 Z= 0.278 Chirality : 0.040 0.354 1384 Planarity : 0.003 0.043 1460 Dihedral : 11.509 144.736 1422 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.91 % Allowed : 16.03 % Favored : 82.06 % 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: -0.76 (0.26), residues: 1046 helix: 0.04 (0.20), residues: 646 sheet: -1.42 (0.57), residues: 68 loop : -1.14 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 147 TYR 0.007 0.001 TYR B 62 PHE 0.010 0.001 PHE C 207 TRP 0.012 0.001 TRP A 50 HIS 0.006 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 8772) covalent geometry : angle 0.57385 (11928) hydrogen bonds : bond 0.03307 ( 458) hydrogen bonds : angle 4.33295 ( 1326) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7713 (tp40) cc_final: 0.7474 (tp-100) REVERT: A 198 LEU cc_start: 0.8652 (tp) cc_final: 0.7934 (tt) REVERT: B 198 LEU cc_start: 0.8646 (tp) cc_final: 0.7926 (tt) REVERT: C 23 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6797 (tt) REVERT: C 112 TYR cc_start: 0.7758 (OUTLIER) cc_final: 0.5924 (t80) REVERT: D 23 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6926 (tt) REVERT: D 112 TYR cc_start: 0.7712 (OUTLIER) cc_final: 0.5819 (t80) outliers start: 17 outliers final: 11 residues processed: 146 average time/residue: 0.2319 time to fit residues: 45.7049 Evaluate side-chains 148 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 207 PHE Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 229 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 69 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.216283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.176310 restraints weight = 30843.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.175590 restraints weight = 25505.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.178624 restraints weight = 20014.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.178862 restraints weight = 16163.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.179229 restraints weight = 13425.692| |-----------------------------------------------------------------------------| r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8772 Z= 0.137 Angle : 0.584 6.333 11928 Z= 0.285 Chirality : 0.040 0.356 1384 Planarity : 0.003 0.043 1460 Dihedral : 11.537 151.063 1422 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.79 % Allowed : 16.48 % Favored : 81.73 % 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: -0.78 (0.26), residues: 1046 helix: 0.03 (0.20), residues: 646 sheet: -1.43 (0.58), residues: 68 loop : -1.17 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 217 TYR 0.008 0.001 TYR A 101 PHE 0.009 0.001 PHE C 207 TRP 0.012 0.001 TRP B 50 HIS 0.005 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8772) covalent geometry : angle 0.58359 (11928) hydrogen bonds : bond 0.03378 ( 458) hydrogen bonds : angle 4.32443 ( 1326) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 LEU cc_start: 0.8710 (tp) cc_final: 0.8030 (tt) REVERT: B 198 LEU cc_start: 0.8694 (tp) cc_final: 0.8013 (tt) REVERT: C 23 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6794 (tt) REVERT: C 112 TYR cc_start: 0.7665 (OUTLIER) cc_final: 0.5747 (t80) REVERT: D 23 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6992 (tt) REVERT: D 112 TYR cc_start: 0.7671 (OUTLIER) cc_final: 0.5754 (t80) outliers start: 16 outliers final: 12 residues processed: 147 average time/residue: 0.2210 time to fit residues: 43.9151 Evaluate side-chains 151 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 207 PHE Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 229 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 50 optimal weight: 0.2980 chunk 55 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.216118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.175503 restraints weight = 30935.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.175283 restraints weight = 19892.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.175661 restraints weight = 16031.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.175990 restraints weight = 13581.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.176267 restraints weight = 13013.987| |-----------------------------------------------------------------------------| r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8772 Z= 0.139 Angle : 0.578 6.062 11928 Z= 0.283 Chirality : 0.040 0.334 1384 Planarity : 0.003 0.043 1460 Dihedral : 11.542 155.370 1422 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.91 % Allowed : 15.47 % Favored : 81.61 % 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: -0.75 (0.26), residues: 1046 helix: 0.04 (0.21), residues: 648 sheet: -1.47 (0.58), residues: 68 loop : -1.13 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 147 TYR 0.008 0.001 TYR B 101 PHE 0.009 0.001 PHE C 207 TRP 0.012 0.001 TRP B 50 HIS 0.005 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8772) covalent geometry : angle 0.57786 (11928) hydrogen bonds : bond 0.03330 ( 458) hydrogen bonds : angle 4.31027 ( 1326) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 LEU cc_start: 0.8694 (tp) cc_final: 0.8058 (tt) REVERT: B 198 LEU cc_start: 0.8684 (tp) cc_final: 0.8013 (tt) REVERT: C 23 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6831 (tt) REVERT: C 112 TYR cc_start: 0.7691 (OUTLIER) cc_final: 0.5802 (t80) REVERT: D 112 TYR cc_start: 0.7712 (OUTLIER) cc_final: 0.5806 (t80) REVERT: D 177 ASP cc_start: 0.7943 (t0) cc_final: 0.7631 (t0) outliers start: 26 outliers final: 19 residues processed: 159 average time/residue: 0.2180 time to fit residues: 47.0014 Evaluate side-chains 158 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 207 PHE Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 229 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 10 optimal weight: 0.2980 chunk 102 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 45 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 47 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.217898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.178736 restraints weight = 30791.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.178115 restraints weight = 22612.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.181354 restraints weight = 18998.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.181790 restraints weight = 15042.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.181959 restraints weight = 12044.180| |-----------------------------------------------------------------------------| r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8772 Z= 0.108 Angle : 0.557 5.536 11928 Z= 0.272 Chirality : 0.039 0.285 1384 Planarity : 0.003 0.042 1460 Dihedral : 11.432 157.387 1422 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.03 % Allowed : 15.92 % Favored : 81.05 % 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: -0.61 (0.27), residues: 1046 helix: 0.17 (0.21), residues: 650 sheet: -1.45 (0.58), residues: 68 loop : -1.11 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 147 TYR 0.007 0.001 TYR B 62 PHE 0.009 0.001 PHE D 207 TRP 0.012 0.001 TRP B 50 HIS 0.005 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 8772) covalent geometry : angle 0.55743 (11928) hydrogen bonds : bond 0.03126 ( 458) hydrogen bonds : angle 4.20774 ( 1326) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 LEU cc_start: 0.8667 (tp) cc_final: 0.8030 (tt) REVERT: C 23 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6816 (tt) REVERT: C 112 TYR cc_start: 0.7646 (OUTLIER) cc_final: 0.5744 (t80) REVERT: D 112 TYR cc_start: 0.7669 (OUTLIER) cc_final: 0.5761 (t80) REVERT: D 177 ASP cc_start: 0.7923 (t0) cc_final: 0.7605 (t0) outliers start: 27 outliers final: 21 residues processed: 157 average time/residue: 0.2160 time to fit residues: 46.2734 Evaluate side-chains 160 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 207 PHE Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 229 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 65 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.212212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.170116 restraints weight = 31083.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.170601 restraints weight = 18598.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.170911 restraints weight = 13771.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.171554 restraints weight = 12841.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.171722 restraints weight = 12315.087| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8772 Z= 0.230 Angle : 0.662 7.058 11928 Z= 0.332 Chirality : 0.043 0.383 1384 Planarity : 0.004 0.043 1460 Dihedral : 12.010 159.301 1422 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.69 % Allowed : 16.26 % Favored : 81.05 % 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: -1.08 (0.26), residues: 1046 helix: -0.20 (0.20), residues: 648 sheet: -1.62 (0.59), residues: 68 loop : -1.32 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 147 TYR 0.022 0.001 TYR B 142 PHE 0.013 0.002 PHE B 248 TRP 0.016 0.002 TRP A 50 HIS 0.006 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00536 ( 8772) covalent geometry : angle 0.66164 (11928) hydrogen bonds : bond 0.03885 ( 458) hydrogen bonds : angle 4.56839 ( 1326) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 LEU cc_start: 0.8733 (tp) cc_final: 0.8051 (tt) REVERT: C 23 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.7038 (tt) REVERT: C 112 TYR cc_start: 0.7859 (OUTLIER) cc_final: 0.5981 (t80) REVERT: C 177 ASP cc_start: 0.7955 (t0) cc_final: 0.7686 (t0) REVERT: C 204 MET cc_start: 0.8285 (tpp) cc_final: 0.8053 (tpp) REVERT: D 112 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.6004 (t80) REVERT: D 204 MET cc_start: 0.8292 (tpp) cc_final: 0.8066 (tpp) outliers start: 24 outliers final: 20 residues processed: 153 average time/residue: 0.2117 time to fit residues: 44.0530 Evaluate side-chains 158 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 207 PHE Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 229 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 0.0170 chunk 5 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.216833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.176477 restraints weight = 30760.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.176512 restraints weight = 19155.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.177122 restraints weight = 15783.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.177316 restraints weight = 13547.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.177653 restraints weight = 12867.024| |-----------------------------------------------------------------------------| r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8772 Z= 0.110 Angle : 0.563 5.580 11928 Z= 0.275 Chirality : 0.039 0.274 1384 Planarity : 0.003 0.043 1460 Dihedral : 11.611 162.255 1422 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.24 % Allowed : 16.59 % Favored : 81.17 % 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: -0.70 (0.27), residues: 1046 helix: 0.08 (0.21), residues: 646 sheet: -1.54 (0.58), residues: 68 loop : -1.09 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 21 TYR 0.011 0.001 TYR B 142 PHE 0.013 0.001 PHE D 207 TRP 0.010 0.001 TRP A 50 HIS 0.005 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 8772) covalent geometry : angle 0.56337 (11928) hydrogen bonds : bond 0.03182 ( 458) hydrogen bonds : angle 4.27300 ( 1326) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 21 ARG cc_start: 0.6747 (mtt180) cc_final: 0.6496 (mtt180) REVERT: C 112 TYR cc_start: 0.7842 (OUTLIER) cc_final: 0.6012 (t80) REVERT: C 177 ASP cc_start: 0.7891 (t0) cc_final: 0.7606 (t0) REVERT: D 112 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.5931 (t80) outliers start: 20 outliers final: 17 residues processed: 154 average time/residue: 0.2113 time to fit residues: 44.2627 Evaluate side-chains 155 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 229 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 22 optimal weight: 0.1980 chunk 100 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.214725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.172853 restraints weight = 31055.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.175017 restraints weight = 15054.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.174615 restraints weight = 11862.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.174773 restraints weight = 11707.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.174881 restraints weight = 11240.953| |-----------------------------------------------------------------------------| r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8772 Z= 0.162 Angle : 0.604 5.633 11928 Z= 0.298 Chirality : 0.040 0.314 1384 Planarity : 0.003 0.042 1460 Dihedral : 11.664 162.823 1422 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.35 % Allowed : 17.38 % Favored : 80.27 % 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: -0.83 (0.27), residues: 1046 helix: 0.01 (0.21), residues: 650 sheet: -1.65 (0.58), residues: 68 loop : -1.20 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 21 TYR 0.018 0.001 TYR A 142 PHE 0.013 0.001 PHE D 207 TRP 0.013 0.001 TRP A 50 HIS 0.006 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 8772) covalent geometry : angle 0.60385 (11928) hydrogen bonds : bond 0.03433 ( 458) hydrogen bonds : angle 4.37053 ( 1326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2588.69 seconds wall clock time: 44 minutes 41.22 seconds (2681.22 seconds total)