Starting phenix.real_space_refine on Mon Apr 6 08:56:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qh1_53152/04_2026/9qh1_53152_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qh1_53152/04_2026/9qh1_53152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qh1_53152/04_2026/9qh1_53152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qh1_53152/04_2026/9qh1_53152.map" model { file = "/net/cci-nas-00/data/ceres_data/9qh1_53152/04_2026/9qh1_53152_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qh1_53152/04_2026/9qh1_53152_trim.cif" } resolution = 3.44 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= 0.037 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 32 5.16 5 C 5444 2.51 5 N 1446 2.21 5 O 1474 1.98 5 H 8526 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: 16930 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 4403 Classifications: {'peptide': 263} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 250} Chain: "B" Number of atoms: 4403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 4403 Classifications: {'peptide': 263} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 250} 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: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.88, per 1000 atoms: 0.17 Number of scatterers: 16930 At special positions: 0 Unit cell: (84.5, 84.5, 113.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 32 16.00 P 6 15.00 Mg 2 11.99 O 1474 8.00 N 1446 7.00 C 5444 6.00 H 8526 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: 1.44 Conformation dependent library (CDL) restraints added in 683.1 milliseconds 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1932 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 4 sheets defined 66.5% alpha, 10.5% 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 35 through 46 Processing helix chain 'A' and resid 46 through 60 removed outlier: 4.070A pdb=" N GLN A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 87 removed outlier: 4.413A pdb=" N THR A 73 " --> pdb=" O PRO A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 121 Proline residue: A 100 - end of helix removed outlier: 3.638A pdb=" N LEU A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 128 through 133 Processing helix chain 'A' and resid 137 through 166 removed outlier: 3.796A pdb=" N VAL A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ILE A 158 " --> pdb=" O HIS A 154 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N PHE A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL A 165 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 176 through 202 removed outlier: 3.931A pdb=" N SER A 192 " --> pdb=" O CYS A 188 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 217 removed outlier: 3.682A pdb=" N GLN A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 231 removed outlier: 4.066A pdb=" N LEU A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 removed outlier: 3.719A pdb=" N VAL A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 258 removed outlier: 4.240A pdb=" N HIS A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 4.015A 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: 4.100A pdb=" N TRP A 266 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 3.681A 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 35 through 46 Processing helix chain 'B' and resid 46 through 60 removed outlier: 4.070A pdb=" N GLN B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 87 removed outlier: 4.413A pdb=" N THR B 73 " --> pdb=" O PRO B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 121 Proline residue: B 100 - end of helix removed outlier: 3.638A pdb=" N LEU B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 128 through 133 Processing helix chain 'B' and resid 137 through 166 removed outlier: 3.795A pdb=" N VAL B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ILE B 158 " --> pdb=" O HIS B 154 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N PHE B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL B 165 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 175 Processing helix chain 'B' and resid 176 through 202 removed outlier: 3.931A pdb=" N SER B 192 " --> pdb=" O CYS B 188 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 217 removed outlier: 3.682A pdb=" N GLN B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 231 removed outlier: 4.066A pdb=" N LEU B 229 " --> pdb=" O ASN B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 240 removed outlier: 3.719A pdb=" N VAL B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 258 removed outlier: 4.240A pdb=" N HIS B 247 " --> pdb=" O ASN B 243 " (cutoff:3.500A) removed outlier: 4.014A 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: 4.100A pdb=" N TRP B 266 " --> pdb=" O GLN B 262 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 279 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 3.681A 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 72 through 80 Processing helix chain 'C' and resid 110 through 121 removed outlier: 3.930A pdb=" N ILE C 116 " --> pdb=" O TYR C 112 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 141 removed outlier: 4.223A pdb=" N ALA C 131 " --> pdb=" O LYS C 127 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ASP C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU C 135 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU C 141 " --> pdb=" O ALA C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 148 Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.555A pdb=" N THR C 152 " --> pdb=" O PRO C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 168 Processing helix chain 'C' and resid 179 through 183 Processing helix chain 'C' and resid 184 through 202 removed outlier: 4.297A pdb=" N LYS C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE C 193 " --> pdb=" O LYS C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 219 removed outlier: 3.907A pdb=" N ARG C 217 " --> pdb=" O GLU C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 244 Processing helix chain 'C' and resid 245 through 263 Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 110 through 121 removed outlier: 3.930A pdb=" N ILE D 116 " --> pdb=" O TYR D 112 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 141 removed outlier: 4.223A pdb=" N ALA D 131 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ASP D 134 " --> pdb=" O GLN D 130 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU D 141 " --> pdb=" O ALA D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 148 Processing helix chain 'D' and resid 149 through 153 removed outlier: 3.555A pdb=" N THR D 152 " --> pdb=" O PRO D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 168 Processing helix chain 'D' and resid 179 through 183 Processing helix chain 'D' and resid 184 through 202 removed outlier: 4.297A pdb=" N LYS D 190 " --> pdb=" O GLU D 186 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE D 193 " --> pdb=" O LYS D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 219 removed outlier: 3.907A pdb=" N ARG D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 244 Processing helix chain 'D' and resid 245 through 263 Processing sheet with id=AA1, first strand: chain 'C' and resid 34 through 37 removed outlier: 3.910A pdb=" N ALA C 34 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU C 46 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL C 43 " --> pdb=" O ILE C 15 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL C 11 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG C 49 " --> pdb=" O ALA C 9 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA C 9 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE C 51 " --> pdb=" O HIS C 7 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N HIS C 7 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU C 53 " --> pdb=" O GLN C 5 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLN C 5 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU C 55 " --> pdb=" O SER C 3 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SER C 3 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER C 3 " --> pdb=" O LYS C 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 95 through 98 removed outlier: 3.838A pdb=" N LEU C 175 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LEU C 174 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ALA C 208 " --> pdb=" O LEU C 174 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LEU C 176 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL C 61 " --> pdb=" O PHE C 207 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLY C 62 " --> pdb=" O MET C 223 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ILE C 225 " --> pdb=" O GLY C 62 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL C 64 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET C 232 " --> pdb=" O TRP C 224 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASP C 226 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ILE C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 34 through 37 removed outlier: 3.910A pdb=" N ALA D 34 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU D 46 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL D 43 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL D 11 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG D 49 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA D 9 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE D 51 " --> pdb=" O HIS D 7 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N HIS D 7 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU D 53 " --> pdb=" O GLN D 5 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLN D 5 " --> pdb=" O LEU D 53 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU D 55 " --> pdb=" O SER D 3 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SER D 3 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER D 3 " --> pdb=" O LYS D 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 95 through 98 removed outlier: 3.838A pdb=" N LEU D 175 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LEU D 174 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ALA D 208 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU D 176 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL D 61 " --> pdb=" O PHE D 207 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLY D 62 " --> pdb=" O MET D 223 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ILE D 225 " --> pdb=" O GLY D 62 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL D 64 " --> pdb=" O ILE D 225 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET D 232 " --> pdb=" O TRP D 224 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASP D 226 " --> pdb=" O ILE D 230 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ILE D 230 " --> pdb=" O ASP D 226 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1320 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: 3.38 Time building geometry restraints manager: 2.05 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: 8522 1.03 - 1.23: 12 1.23 - 1.42: 3590 1.42 - 1.62: 4942 1.62 - 1.81: 60 Bond restraints: 17126 Sorted by residual: bond pdb=" CB ILE B 72 " pdb=" HB ILE B 72 " ideal model delta sigma weight residual 0.970 0.879 0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" CB ILE A 72 " pdb=" HB ILE A 72 " ideal model delta sigma weight residual 0.970 0.879 0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" C1' ATP C 502 " pdb=" C2' ATP C 502 " ideal model delta sigma weight residual 1.531 1.518 0.013 1.20e-02 6.94e+03 1.17e+00 bond pdb=" C1' ATP D 502 " pdb=" C2' ATP D 502 " ideal model delta sigma weight residual 1.531 1.518 0.013 1.20e-02 6.94e+03 1.17e+00 bond pdb=" CB MET A 228 " pdb=" CG MET A 228 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.09e+00 ... (remaining 17121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.98: 30914 3.98 - 7.96: 76 7.96 - 11.94: 2 11.94 - 15.92: 2 15.92 - 19.89: 2 Bond angle restraints: 30996 Sorted by residual: angle pdb=" CA ILE B 72 " pdb=" CB ILE B 72 " pdb=" HB ILE B 72 " ideal model delta sigma weight residual 109.00 89.11 19.89 3.00e+00 1.11e-01 4.40e+01 angle pdb=" CA ILE A 72 " pdb=" CB ILE A 72 " pdb=" HB ILE A 72 " ideal model delta sigma weight residual 109.00 89.12 19.88 3.00e+00 1.11e-01 4.39e+01 angle pdb=" CG1 ILE B 72 " pdb=" CB ILE B 72 " pdb=" HB ILE B 72 " ideal model delta sigma weight residual 109.00 121.55 -12.55 3.00e+00 1.11e-01 1.75e+01 angle pdb=" CG1 ILE A 72 " pdb=" CB ILE A 72 " pdb=" HB ILE A 72 " ideal model delta sigma weight residual 109.00 121.55 -12.55 3.00e+00 1.11e-01 1.75e+01 angle pdb=" NE ARG A 285 " pdb=" CD ARG A 285 " pdb=" HD2 ARG A 285 " ideal model delta sigma weight residual 108.00 116.91 -8.91 3.00e+00 1.11e-01 8.83e+00 ... (remaining 30991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 6968 17.60 - 35.21: 670 35.21 - 52.81: 250 52.81 - 70.42: 68 70.42 - 88.02: 22 Dihedral angle restraints: 7978 sinusoidal: 4362 harmonic: 3616 Sorted by residual: dihedral pdb=" CA GLU B 127 " pdb=" C GLU B 127 " pdb=" N GLY B 128 " pdb=" CA GLY B 128 " ideal model delta harmonic sigma weight residual 180.00 -154.01 -25.99 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA GLU A 127 " pdb=" C GLU A 127 " pdb=" N GLY A 128 " pdb=" CA GLY A 128 " ideal model delta harmonic sigma weight residual -180.00 -154.01 -25.99 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA ALA D 26 " pdb=" C ALA D 26 " pdb=" N PHE D 27 " pdb=" CA PHE D 27 " ideal model delta harmonic sigma weight residual -180.00 -155.95 -24.05 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 7975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1092 0.057 - 0.114: 215 0.114 - 0.171: 25 0.171 - 0.228: 0 0.228 - 0.285: 6 Chirality restraints: 1338 Sorted by residual: chirality pdb=" C2' ATP D 502 " pdb=" C1' ATP D 502 " pdb=" C3' ATP D 502 " pdb=" O2' ATP D 502 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C2' ATP C 502 " pdb=" C1' ATP C 502 " pdb=" C3' ATP C 502 " pdb=" O2' ATP C 502 " both_signs ideal model delta sigma weight residual False -2.68 -2.96 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C3' ATP D 502 " pdb=" C2' ATP D 502 " pdb=" C4' ATP D 502 " pdb=" O3' ATP D 502 " both_signs ideal model delta sigma weight residual False -2.63 -2.89 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 1335 not shown) Planarity restraints: 2464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 76 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.70e+00 pdb=" C THR B 76 " -0.041 2.00e-02 2.50e+03 pdb=" O THR B 76 " 0.016 2.00e-02 2.50e+03 pdb=" N GLY B 77 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 76 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.70e+00 pdb=" C THR A 76 " 0.041 2.00e-02 2.50e+03 pdb=" O THR A 76 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY A 77 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 79 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.57e+00 pdb=" C THR A 79 " -0.041 2.00e-02 2.50e+03 pdb=" O THR A 79 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA A 80 " 0.014 2.00e-02 2.50e+03 ... (remaining 2461 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 138 2.10 - 2.73: 29289 2.73 - 3.35: 49536 3.35 - 3.98: 61103 3.98 - 4.60: 97802 Nonbonded interactions: 237868 Sorted by model distance: nonbonded pdb="HH22 ARG A 61 " pdb=" HB ILE A 72 " model vdw 1.478 2.270 nonbonded pdb="HH22 ARG B 61 " pdb=" HB ILE B 72 " model vdw 1.478 2.270 nonbonded pdb="HH21 ARG A 61 " pdb=" HB ILE A 72 " model vdw 1.738 2.270 nonbonded pdb="HH21 ARG B 61 " pdb=" HB ILE B 72 " model vdw 1.738 2.270 nonbonded pdb=" NH2 ARG B 61 " pdb=" HB ILE B 72 " model vdw 1.790 2.770 ... (remaining 237863 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.300 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 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 0.041 8600 Z= 0.186 Angle : 0.773 7.833 11698 Z= 0.420 Chirality : 0.047 0.285 1338 Planarity : 0.005 0.049 1454 Dihedral : 17.027 88.024 3138 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 15.32 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.23), residues: 1042 helix: -1.40 (0.18), residues: 618 sheet: -2.17 (0.54), residues: 78 loop : -1.68 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 253 TYR 0.012 0.002 TYR D 243 PHE 0.012 0.002 PHE D 121 TRP 0.011 0.001 TRP B 50 HIS 0.023 0.002 HIS C 251 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 8600) covalent geometry : angle 0.77327 (11698) hydrogen bonds : bond 0.19019 ( 458) hydrogen bonds : angle 7.74717 ( 1320) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7357 (ptt90) cc_final: 0.6713 (ttp-110) REVERT: A 50 TRP cc_start: 0.7742 (p-90) cc_final: 0.7536 (p-90) REVERT: A 132 GLN cc_start: 0.7566 (mt0) cc_final: 0.7313 (mt0) REVERT: B 38 ARG cc_start: 0.7361 (ptt90) cc_final: 0.6714 (ttp-110) REVERT: B 50 TRP cc_start: 0.7743 (p-90) cc_final: 0.7534 (p-90) REVERT: B 132 GLN cc_start: 0.7553 (mt0) cc_final: 0.7303 (mt0) REVERT: C 113 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7252 (mt-10) REVERT: D 113 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7252 (mt-10) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2435 time to fit residues: 40.6272 Evaluate side-chains 114 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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: 0.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 187 ASN A 225 ASN B 169 HIS B 187 ASN B 225 ASN C 196 GLN D 196 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.169480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.146649 restraints weight = 29228.386| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 1.98 r_work: 0.3651 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8600 Z= 0.154 Angle : 0.538 5.411 11698 Z= 0.294 Chirality : 0.040 0.141 1338 Planarity : 0.004 0.047 1454 Dihedral : 8.387 66.620 1210 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.80 % Allowed : 15.77 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.25), residues: 1042 helix: -0.40 (0.20), residues: 642 sheet: -2.30 (0.54), residues: 78 loop : -1.45 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 285 TYR 0.006 0.001 TYR B 87 PHE 0.012 0.001 PHE B 159 TRP 0.010 0.001 TRP B 50 HIS 0.006 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 8600) covalent geometry : angle 0.53816 (11698) hydrogen bonds : bond 0.04579 ( 458) hydrogen bonds : angle 4.91041 ( 1320) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7462 (ptt90) cc_final: 0.6800 (ttp-110) REVERT: A 57 ASP cc_start: 0.7339 (t0) cc_final: 0.7112 (t0) REVERT: A 61 ARG cc_start: 0.7946 (ttp80) cc_final: 0.7482 (ttp80) REVERT: B 38 ARG cc_start: 0.7479 (ptt90) cc_final: 0.6800 (ttp-110) REVERT: B 57 ASP cc_start: 0.7336 (t0) cc_final: 0.7112 (t0) REVERT: B 61 ARG cc_start: 0.7958 (ttp80) cc_final: 0.7490 (ttp80) REVERT: C 113 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7438 (mt-10) REVERT: C 129 MET cc_start: 0.7362 (mmm) cc_final: 0.6946 (mmt) REVERT: C 142 LEU cc_start: 0.6947 (mp) cc_final: 0.6411 (mp) REVERT: D 113 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7440 (mt-10) REVERT: D 129 MET cc_start: 0.7286 (mmm) cc_final: 0.6870 (mmt) REVERT: D 142 LEU cc_start: 0.6937 (mp) cc_final: 0.6404 (mp) outliers start: 16 outliers final: 12 residues processed: 130 average time/residue: 0.2512 time to fit residues: 42.8204 Evaluate side-chains 126 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 192 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 85 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 GLN D 196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.165381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.142303 restraints weight = 30131.940| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.03 r_work: 0.3607 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8600 Z= 0.174 Angle : 0.541 4.825 11698 Z= 0.296 Chirality : 0.040 0.139 1338 Planarity : 0.004 0.048 1454 Dihedral : 8.181 65.769 1210 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.48 % Allowed : 16.44 % Favored : 81.08 % 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: -1.35 (0.25), residues: 1042 helix: -0.31 (0.20), residues: 652 sheet: -2.31 (0.56), residues: 78 loop : -1.49 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 63 TYR 0.008 0.001 TYR D 153 PHE 0.013 0.002 PHE D 27 TRP 0.012 0.001 TRP A 50 HIS 0.006 0.001 HIS C 251 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 8600) covalent geometry : angle 0.54071 (11698) hydrogen bonds : bond 0.04295 ( 458) hydrogen bonds : angle 4.73736 ( 1320) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7485 (ptt90) cc_final: 0.6670 (ttp-110) REVERT: A 57 ASP cc_start: 0.7476 (t0) cc_final: 0.7204 (t0) REVERT: A 83 MET cc_start: 0.8007 (mtm) cc_final: 0.7553 (mtp) REVERT: B 38 ARG cc_start: 0.7481 (ptt90) cc_final: 0.6654 (ttp-110) REVERT: B 57 ASP cc_start: 0.7456 (t0) cc_final: 0.7182 (t0) REVERT: B 83 MET cc_start: 0.8017 (mtm) cc_final: 0.7721 (mtp) REVERT: C 112 TYR cc_start: 0.7649 (m-80) cc_final: 0.7399 (m-80) REVERT: C 129 MET cc_start: 0.7991 (mmm) cc_final: 0.7062 (mmt) REVERT: D 112 TYR cc_start: 0.7674 (m-80) cc_final: 0.7392 (m-80) REVERT: D 129 MET cc_start: 0.7991 (mmm) cc_final: 0.7069 (mmt) outliers start: 22 outliers final: 16 residues processed: 138 average time/residue: 0.2337 time to fit residues: 42.7016 Evaluate side-chains 131 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 190 TRP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 190 TRP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 192 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 45 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 95 optimal weight: 0.0980 chunk 103 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 GLN D 196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.167509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.144141 restraints weight = 29748.443| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.04 r_work: 0.3628 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8600 Z= 0.117 Angle : 0.486 4.518 11698 Z= 0.262 Chirality : 0.039 0.139 1338 Planarity : 0.004 0.048 1454 Dihedral : 8.044 63.952 1210 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.03 % Allowed : 16.89 % Favored : 81.08 % 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: -0.99 (0.26), residues: 1042 helix: -0.03 (0.20), residues: 656 sheet: -2.19 (0.57), residues: 78 loop : -1.35 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 63 TYR 0.006 0.001 TYR A 101 PHE 0.012 0.001 PHE C 27 TRP 0.013 0.001 TRP A 50 HIS 0.007 0.001 HIS C 251 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8600) covalent geometry : angle 0.48603 (11698) hydrogen bonds : bond 0.03633 ( 458) hydrogen bonds : angle 4.41016 ( 1320) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7345 (ptt90) cc_final: 0.6607 (ttp-110) REVERT: B 38 ARG cc_start: 0.7338 (ptt90) cc_final: 0.6590 (ttp-110) REVERT: B 63 ARG cc_start: 0.7896 (mmm-85) cc_final: 0.7478 (mmm-85) REVERT: C 129 MET cc_start: 0.8038 (mmm) cc_final: 0.7111 (mmt) REVERT: D 129 MET cc_start: 0.8051 (mmm) cc_final: 0.7130 (mmt) outliers start: 18 outliers final: 18 residues processed: 142 average time/residue: 0.2435 time to fit residues: 45.8907 Evaluate side-chains 138 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 190 TRP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 190 TRP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 192 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 GLN D 196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.164783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.142001 restraints weight = 29997.042| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.00 r_work: 0.3609 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8600 Z= 0.146 Angle : 0.500 4.562 11698 Z= 0.272 Chirality : 0.039 0.139 1338 Planarity : 0.004 0.048 1454 Dihedral : 8.026 63.814 1210 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.14 % Allowed : 17.00 % Favored : 80.86 % 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: -1.00 (0.26), residues: 1042 helix: 0.02 (0.20), residues: 644 sheet: -2.19 (0.57), residues: 78 loop : -1.44 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 63 TYR 0.007 0.001 TYR B 62 PHE 0.014 0.001 PHE C 27 TRP 0.012 0.001 TRP B 50 HIS 0.008 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8600) covalent geometry : angle 0.49986 (11698) hydrogen bonds : bond 0.03692 ( 458) hydrogen bonds : angle 4.42153 ( 1320) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7422 (ptt90) cc_final: 0.6660 (ttp-110) REVERT: B 38 ARG cc_start: 0.7420 (ptt90) cc_final: 0.6648 (ttp-110) REVERT: B 63 ARG cc_start: 0.7816 (mmm-85) cc_final: 0.7375 (mmm-85) REVERT: C 129 MET cc_start: 0.8051 (mmm) cc_final: 0.7230 (mmt) REVERT: D 129 MET cc_start: 0.8044 (mmm) cc_final: 0.7234 (mmt) outliers start: 19 outliers final: 17 residues processed: 148 average time/residue: 0.2376 time to fit residues: 46.6941 Evaluate side-chains 143 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 190 TRP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 190 TRP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 174 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 54 optimal weight: 0.3980 chunk 102 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 63 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 GLN D 196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.164619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.141955 restraints weight = 29977.893| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.98 r_work: 0.3612 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8600 Z= 0.139 Angle : 0.496 4.549 11698 Z= 0.269 Chirality : 0.039 0.137 1338 Planarity : 0.004 0.047 1454 Dihedral : 8.087 64.419 1210 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.25 % Allowed : 17.79 % Favored : 79.95 % 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: -1.04 (0.26), residues: 1042 helix: -0.02 (0.20), residues: 656 sheet: -2.38 (0.49), residues: 98 loop : -1.29 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 61 TYR 0.006 0.001 TYR B 87 PHE 0.014 0.001 PHE C 27 TRP 0.013 0.001 TRP B 50 HIS 0.008 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8600) covalent geometry : angle 0.49584 (11698) hydrogen bonds : bond 0.03594 ( 458) hydrogen bonds : angle 4.37576 ( 1320) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.329 Fit side-chains REVERT: A 38 ARG cc_start: 0.7411 (ptt90) cc_final: 0.6658 (ttp-110) REVERT: B 38 ARG cc_start: 0.7419 (ptt90) cc_final: 0.6646 (ttp-110) REVERT: B 63 ARG cc_start: 0.7811 (mmm-85) cc_final: 0.7409 (mmm-85) outliers start: 20 outliers final: 20 residues processed: 137 average time/residue: 0.2362 time to fit residues: 42.6703 Evaluate side-chains 139 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 190 TRP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 190 TRP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 192 ARG Chi-restraints excluded: chain D residue 221 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 99 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 GLN D 196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.165098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.142574 restraints weight = 29842.075| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.97 r_work: 0.3619 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8600 Z= 0.123 Angle : 0.489 4.784 11698 Z= 0.263 Chirality : 0.039 0.136 1338 Planarity : 0.004 0.053 1454 Dihedral : 8.106 66.347 1210 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.14 % Allowed : 18.24 % Favored : 79.62 % 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: -0.88 (0.26), residues: 1042 helix: 0.08 (0.20), residues: 656 sheet: -2.31 (0.49), residues: 98 loop : -1.19 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 63 TYR 0.006 0.001 TYR A 87 PHE 0.013 0.001 PHE C 27 TRP 0.014 0.001 TRP A 50 HIS 0.009 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8600) covalent geometry : angle 0.48946 (11698) hydrogen bonds : bond 0.03447 ( 458) hydrogen bonds : angle 4.30703 ( 1320) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.310 Fit side-chains REVERT: A 38 ARG cc_start: 0.7430 (ptt90) cc_final: 0.6687 (ttp-110) REVERT: A 63 ARG cc_start: 0.7945 (mmm-85) cc_final: 0.7584 (mmm-85) REVERT: B 38 ARG cc_start: 0.7432 (ptt90) cc_final: 0.6676 (ttp-110) REVERT: B 63 ARG cc_start: 0.7796 (mmm-85) cc_final: 0.7384 (mmm-85) outliers start: 19 outliers final: 17 residues processed: 131 average time/residue: 0.2205 time to fit residues: 38.1443 Evaluate side-chains 134 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 190 TRP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 190 TRP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 192 ARG Chi-restraints excluded: chain D residue 221 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 33 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN B 60 GLN C 196 GLN D 196 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.166057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.143280 restraints weight = 29901.613| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.99 r_work: 0.3625 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8600 Z= 0.108 Angle : 0.481 5.026 11698 Z= 0.257 Chirality : 0.038 0.136 1338 Planarity : 0.004 0.048 1454 Dihedral : 8.070 68.293 1210 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.25 % Allowed : 18.02 % Favored : 79.73 % 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: -0.74 (0.26), residues: 1042 helix: 0.19 (0.20), residues: 656 sheet: -2.26 (0.49), residues: 98 loop : -1.12 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 63 TYR 0.005 0.001 TYR B 87 PHE 0.011 0.001 PHE C 27 TRP 0.015 0.001 TRP A 50 HIS 0.011 0.001 HIS C 251 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8600) covalent geometry : angle 0.48105 (11698) hydrogen bonds : bond 0.03294 ( 458) hydrogen bonds : angle 4.23633 ( 1320) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.474 Fit side-chains REVERT: A 38 ARG cc_start: 0.7434 (ptt90) cc_final: 0.6694 (ttp-110) REVERT: A 63 ARG cc_start: 0.7803 (mmm-85) cc_final: 0.7456 (mmm-85) REVERT: A 201 ARG cc_start: 0.8042 (tpt90) cc_final: 0.7691 (tpt90) REVERT: B 38 ARG cc_start: 0.7419 (ptt90) cc_final: 0.6663 (ttp-110) REVERT: B 63 ARG cc_start: 0.7778 (mmm-85) cc_final: 0.7376 (mmm-85) REVERT: B 201 ARG cc_start: 0.8024 (tpt90) cc_final: 0.7675 (tpt90) outliers start: 20 outliers final: 18 residues processed: 137 average time/residue: 0.2401 time to fit residues: 43.7167 Evaluate side-chains 138 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 190 TRP Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 190 TRP Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 192 ARG Chi-restraints excluded: chain D residue 221 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 97 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 12 optimal weight: 0.0970 chunk 101 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 GLN D 196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.166634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.143863 restraints weight = 29775.216| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.99 r_work: 0.3630 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8600 Z= 0.109 Angle : 0.481 4.521 11698 Z= 0.256 Chirality : 0.038 0.137 1338 Planarity : 0.004 0.048 1454 Dihedral : 8.019 70.272 1210 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.14 % Allowed : 18.92 % Favored : 78.94 % 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: -0.57 (0.26), residues: 1042 helix: 0.27 (0.21), residues: 656 sheet: -2.03 (0.58), residues: 78 loop : -1.09 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 63 TYR 0.005 0.001 TYR B 101 PHE 0.011 0.001 PHE D 27 TRP 0.014 0.001 TRP A 50 HIS 0.011 0.001 HIS C 251 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8600) covalent geometry : angle 0.48096 (11698) hydrogen bonds : bond 0.03229 ( 458) hydrogen bonds : angle 4.18330 ( 1320) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.432 Fit side-chains REVERT: A 38 ARG cc_start: 0.7415 (ptt90) cc_final: 0.6661 (ttp-110) REVERT: A 63 ARG cc_start: 0.7746 (mmm-85) cc_final: 0.7377 (mmm-85) REVERT: A 201 ARG cc_start: 0.7972 (tpt90) cc_final: 0.7618 (tpt90) REVERT: B 38 ARG cc_start: 0.7407 (ptt90) cc_final: 0.6638 (ttp-110) REVERT: B 201 ARG cc_start: 0.7963 (tpt90) cc_final: 0.7616 (tpt90) outliers start: 19 outliers final: 18 residues processed: 128 average time/residue: 0.2422 time to fit residues: 41.0098 Evaluate side-chains 134 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 190 TRP Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 190 TRP Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 192 ARG Chi-restraints excluded: chain D residue 221 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 68 optimal weight: 0.0470 chunk 90 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 GLN D 196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.164482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.141947 restraints weight = 30077.410| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.96 r_work: 0.3610 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8600 Z= 0.144 Angle : 0.512 4.702 11698 Z= 0.273 Chirality : 0.039 0.137 1338 Planarity : 0.004 0.048 1454 Dihedral : 8.082 69.445 1210 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.48 % Allowed : 18.58 % Favored : 78.94 % 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: -0.74 (0.26), residues: 1042 helix: 0.13 (0.20), residues: 656 sheet: -2.08 (0.58), residues: 78 loop : -1.14 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 63 TYR 0.007 0.001 TYR A 293 PHE 0.013 0.001 PHE C 27 TRP 0.013 0.001 TRP B 50 HIS 0.013 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 8600) covalent geometry : angle 0.51193 (11698) hydrogen bonds : bond 0.03422 ( 458) hydrogen bonds : angle 4.28763 ( 1320) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.324 Fit side-chains REVERT: A 38 ARG cc_start: 0.7438 (ptt90) cc_final: 0.6670 (ttp-110) REVERT: A 63 ARG cc_start: 0.7748 (mmm-85) cc_final: 0.7358 (mmm-85) REVERT: A 201 ARG cc_start: 0.8047 (tpt90) cc_final: 0.7724 (tpt90) REVERT: B 38 ARG cc_start: 0.7437 (ptt90) cc_final: 0.6652 (ttp-110) REVERT: B 63 ARG cc_start: 0.7817 (mmm-85) cc_final: 0.7368 (mmm-85) REVERT: B 201 ARG cc_start: 0.8032 (tpt90) cc_final: 0.7705 (tpt90) outliers start: 22 outliers final: 21 residues processed: 130 average time/residue: 0.2387 time to fit residues: 40.8439 Evaluate side-chains 140 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 190 TRP Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 190 TRP Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 192 ARG Chi-restraints excluded: chain D residue 221 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 82 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 23 optimal weight: 0.0570 chunk 77 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 GLN D 196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.166364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.143419 restraints weight = 29844.889| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.01 r_work: 0.3619 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8600 Z= 0.114 Angle : 0.488 4.963 11698 Z= 0.259 Chirality : 0.038 0.136 1338 Planarity : 0.004 0.048 1454 Dihedral : 8.062 70.574 1210 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.25 % Allowed : 18.58 % Favored : 79.17 % 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: -0.64 (0.27), residues: 1042 helix: 0.28 (0.21), residues: 656 sheet: -2.23 (0.50), residues: 98 loop : -1.11 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 63 TYR 0.007 0.001 TYR B 62 PHE 0.011 0.001 PHE C 27 TRP 0.015 0.001 TRP B 50 HIS 0.014 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8600) covalent geometry : angle 0.48771 (11698) hydrogen bonds : bond 0.03221 ( 458) hydrogen bonds : angle 4.18686 ( 1320) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3818.88 seconds wall clock time: 65 minutes 19.63 seconds (3919.63 seconds total)