Starting phenix.real_space_refine on Sun May 3 03:23:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9izg_61032/05_2026/9izg_61032.cif Found real_map, /net/cci-nas-00/data/ceres_data/9izg_61032/05_2026/9izg_61032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9izg_61032/05_2026/9izg_61032.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9izg_61032/05_2026/9izg_61032.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9izg_61032/05_2026/9izg_61032.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9izg_61032/05_2026/9izg_61032.map" } resolution = 3.04 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= -0.003 sd= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2176 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 62 5.16 5 C 5553 2.51 5 N 1483 2.21 5 O 1603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8702 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2492 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 6, 'GLN:plan1': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 82 Chain: "C" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 397 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "R" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2344 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 289} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'ARG:plan': 5, 'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1700 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 6, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 5, 'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 82 Chain: "S" Number of atoms: 1739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1739 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NKP': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 2.32, per 1000 atoms: 0.27 Number of scatterers: 8702 At special positions: 0 Unit cell: (86.24, 116.62, 132.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 62 16.00 P 1 15.00 O 1603 8.00 N 1483 7.00 C 5553 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 188 " - pdb=" SG CYS R 195 " distance=2.03 Simple disulfide: pdb=" SG CYS R 284 " - pdb=" SG CYS R 287 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 274.6 milliseconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2154 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 12 sheets defined 35.6% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.690A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'R' and resid 30 through 37 removed outlier: 4.165A pdb=" N ARG R 36 " --> pdb=" O PHE R 32 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER R 37 " --> pdb=" O PHE R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 77 removed outlier: 3.619A pdb=" N LEU R 55 " --> pdb=" O LEU R 51 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR R 58 " --> pdb=" O GLY R 54 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL R 70 " --> pdb=" O ALA R 66 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET R 71 " --> pdb=" O ASN R 67 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR R 75 " --> pdb=" O MET R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 81 removed outlier: 3.573A pdb=" N HIS R 81 " --> pdb=" O ARG R 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 78 through 81' Processing helix chain 'R' and resid 82 through 107 removed outlier: 3.631A pdb=" N LEU R 87 " --> pdb=" O PRO R 83 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE R 107 " --> pdb=" O PHE R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 152 removed outlier: 3.609A pdb=" N LEU R 123 " --> pdb=" O SER R 119 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE R 128 " --> pdb=" O ARG R 124 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN R 138 " --> pdb=" O ALA R 134 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE R 151 " --> pdb=" O HIS R 147 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 181 removed outlier: 3.876A pdb=" N VAL R 165 " --> pdb=" O ASN R 161 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL R 166 " --> pdb=" O ARG R 162 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL R 169 " --> pdb=" O VAL R 165 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL R 170 " --> pdb=" O VAL R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 237 removed outlier: 3.650A pdb=" N PHE R 213 " --> pdb=" O PHE R 209 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN R 214 " --> pdb=" O TRP R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 246 through 270 removed outlier: 3.505A pdb=" N ARG R 250 " --> pdb=" O PRO R 246 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP R 251 " --> pdb=" O ARG R 247 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE R 267 " --> pdb=" O VAL R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 280 removed outlier: 3.511A pdb=" N LEU R 277 " --> pdb=" O PRO R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 292 through 311 removed outlier: 3.678A pdb=" N LEU R 297 " --> pdb=" O GLU R 293 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU R 298 " --> pdb=" O LYS R 294 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER R 304 " --> pdb=" O ALA R 300 " (cutoff:3.500A) Proline residue: R 308 - end of helix Processing helix chain 'A' and resid 6 through 26 removed outlier: 3.694A pdb=" N ASP A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 49 removed outlier: 4.372A pdb=" N GLY A 45 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS A 46 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N SER A 47 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A 49 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 removed outlier: 3.529A pdb=" N SER A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE A 128 " --> pdb=" O ASP A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 155 removed outlier: 3.561A pdb=" N LEU A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.825A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 183 through 204 removed outlier: 3.699A pdb=" N PHE A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 243 removed outlier: 3.674A pdb=" N MET A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.014A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.542A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.687A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.698A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.187A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.790A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.593A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.039A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.828A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 70 through 76 removed outlier: 3.518A pdb=" N PHE A 74 " --> pdb=" O PHE A 81 " (cutoff:3.500A) removed outlier: 9.514A pdb=" N ALA A 105 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ARG A 35 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ILE A 107 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU A 37 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL A 109 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU A 39 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N ASP A 111 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL A 139 " --> pdb=" O TYR A 212 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N HIS A 214 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU A 141 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.531A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.827A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.753A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1149 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: 1.50 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1528 1.33 - 1.45: 2400 1.45 - 1.57: 4863 1.57 - 1.69: 1 1.69 - 1.82: 93 Bond restraints: 8885 Sorted by residual: bond pdb=" OAD NKP R 601 " pdb=" PAC NKP R 601 " ideal model delta sigma weight residual 1.696 1.511 0.185 2.00e-02 2.50e+03 8.53e+01 bond pdb=" OAB NKP R 601 " pdb=" PAC NKP R 601 " ideal model delta sigma weight residual 1.683 1.514 0.169 2.00e-02 2.50e+03 7.15e+01 bond pdb=" CAK NKP R 601 " pdb=" OAJ NKP R 601 " ideal model delta sigma weight residual 1.380 1.333 0.047 2.00e-02 2.50e+03 5.49e+00 bond pdb=" OAA NKP R 601 " pdb=" PAC NKP R 601 " ideal model delta sigma weight residual 1.472 1.515 -0.043 2.00e-02 2.50e+03 4.52e+00 bond pdb=" CA TYR A 170 " pdb=" C TYR A 170 " ideal model delta sigma weight residual 1.524 1.499 0.025 1.26e-02 6.30e+03 3.95e+00 ... (remaining 8880 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.95: 12085 11.95 - 23.90: 1 23.90 - 35.85: 0 35.85 - 47.81: 0 47.81 - 59.76: 1 Bond angle restraints: 12087 Sorted by residual: angle pdb=" OAB NKP R 601 " pdb=" PAC NKP R 601 " pdb=" OAD NKP R 601 " ideal model delta sigma weight residual 53.21 112.97 -59.76 3.00e+00 1.11e-01 3.97e+02 angle pdb=" C THR A 172 " pdb=" N PRO A 173 " pdb=" CA PRO A 173 " ideal model delta sigma weight residual 119.93 113.84 6.09 1.07e+00 8.73e-01 3.24e+01 angle pdb=" OAA NKP R 601 " pdb=" PAC NKP R 601 " pdb=" OAB NKP R 601 " ideal model delta sigma weight residual 128.27 112.69 15.58 3.00e+00 1.11e-01 2.70e+01 angle pdb=" C GLU B 3 " pdb=" CA GLU B 3 " pdb=" CB GLU B 3 " ideal model delta sigma weight residual 116.63 110.67 5.96 1.16e+00 7.43e-01 2.64e+01 angle pdb=" N GLN B 6 " pdb=" CA GLN B 6 " pdb=" C GLN B 6 " ideal model delta sigma weight residual 111.07 106.29 4.78 1.07e+00 8.73e-01 2.00e+01 ... (remaining 12082 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 4491 17.29 - 34.59: 539 34.59 - 51.88: 169 51.88 - 69.17: 21 69.17 - 86.46: 10 Dihedral angle restraints: 5230 sinusoidal: 1893 harmonic: 3337 Sorted by residual: dihedral pdb=" CB CYS R 284 " pdb=" SG CYS R 284 " pdb=" SG CYS R 287 " pdb=" CB CYS R 287 " ideal model delta sinusoidal sigma weight residual 93.00 170.09 -77.09 1 1.00e+01 1.00e-02 7.45e+01 dihedral pdb=" CB CYS S 22 " pdb=" SG CYS S 22 " pdb=" SG CYS S 96 " pdb=" CB CYS S 96 " ideal model delta sinusoidal sigma weight residual 93.00 64.02 28.98 1 1.00e+01 1.00e-02 1.20e+01 dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 64.16 28.84 1 1.00e+01 1.00e-02 1.19e+01 ... (remaining 5227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1327 0.090 - 0.180: 74 0.180 - 0.270: 1 0.270 - 0.360: 0 0.360 - 0.450: 1 Chirality restraints: 1403 Sorted by residual: chirality pdb=" CAH NKP R 601 " pdb=" CAG NKP R 601 " pdb=" CAI NKP R 601 " pdb=" OBC NKP R 601 " both_signs ideal model delta sigma weight residual False -2.84 -2.39 -0.45 2.00e-01 2.50e+01 5.06e+00 chirality pdb=" CB THR B 47 " pdb=" CA THR B 47 " pdb=" OG1 THR B 47 " pdb=" CG2 THR B 47 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CG LEU R 279 " pdb=" CB LEU R 279 " pdb=" CD1 LEU R 279 " pdb=" CD2 LEU R 279 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.61e-01 ... (remaining 1400 not shown) Planarity restraints: 1529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 54 " -0.025 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO C 55 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 55 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 55 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 114 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" CG ASP A 114 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASP A 114 " 0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP A 114 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER S 106 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.74e+00 pdb=" N PRO S 107 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO S 107 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO S 107 " -0.018 5.00e-02 4.00e+02 ... (remaining 1526 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1543 2.77 - 3.30: 7688 3.30 - 3.83: 14305 3.83 - 4.37: 17056 4.37 - 4.90: 30470 Nonbonded interactions: 71062 Sorted by model distance: nonbonded pdb=" OG SER S 149 " pdb=" O LYS S 151 " model vdw 2.233 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.237 3.040 nonbonded pdb=" OG SER S 7 " pdb=" OG SER S 21 " model vdw 2.246 3.040 nonbonded pdb=" OH TYR R 311 " pdb=" O HOH R 701 " model vdw 2.259 3.040 nonbonded pdb=" OG SER S 106 " pdb=" OD1 ASP S 109 " model vdw 2.271 3.040 ... (remaining 71057 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.710 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 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 0.185 8889 Z= 0.210 Angle : 0.824 59.757 12095 Z= 0.373 Chirality : 0.044 0.450 1403 Planarity : 0.004 0.037 1529 Dihedral : 16.840 86.464 3064 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.45 % Allowed : 26.68 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.33 (0.23), residues: 1133 helix: -1.34 (0.23), residues: 373 sheet: -0.09 (0.31), residues: 276 loop : -0.78 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 185 TYR 0.011 0.001 TYR S 103 PHE 0.015 0.001 PHE B 151 TRP 0.007 0.001 TRP B 169 HIS 0.007 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 8885) covalent geometry : angle 0.82408 (12087) SS BOND : bond 0.00236 ( 4) SS BOND : angle 1.05621 ( 8) hydrogen bonds : bond 0.27973 ( 408) hydrogen bonds : angle 8.38328 ( 1149) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 124 time to evaluate : 0.206 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 127 average time/residue: 0.1096 time to fit residues: 18.6929 Evaluate side-chains 125 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 123 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 318 MET Chi-restraints excluded: chain A residue 171 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 30.0000 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 100 optimal weight: 0.0170 chunk 106 optimal weight: 1.9990 overall best weight: 1.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 90 ASN R 138 ASN R 214 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.159887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.126015 restraints weight = 9944.229| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.84 r_work: 0.3333 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8889 Z= 0.134 Angle : 0.510 5.585 12095 Z= 0.276 Chirality : 0.041 0.139 1403 Planarity : 0.004 0.036 1529 Dihedral : 5.938 59.154 1269 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.91 % Allowed : 25.67 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.03 (0.25), residues: 1133 helix: 0.91 (0.26), residues: 371 sheet: -0.01 (0.30), residues: 278 loop : -0.56 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 185 TYR 0.013 0.001 TYR S 178 PHE 0.013 0.001 PHE B 151 TRP 0.012 0.001 TRP B 169 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8885) covalent geometry : angle 0.50962 (12087) SS BOND : bond 0.00489 ( 4) SS BOND : angle 0.82629 ( 8) hydrogen bonds : bond 0.05560 ( 408) hydrogen bonds : angle 4.75103 ( 1149) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.348 Fit side-chains REVERT: R 279 LEU cc_start: 0.8486 (mm) cc_final: 0.8203 (mm) REVERT: A 10 LYS cc_start: 0.8654 (ttmm) cc_final: 0.8302 (mttp) REVERT: A 17 LYS cc_start: 0.8239 (mttt) cc_final: 0.8020 (mtmt) REVERT: A 21 LYS cc_start: 0.8029 (mmtp) cc_final: 0.7311 (ttpt) REVERT: S 39 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8396 (tt0) outliers start: 26 outliers final: 17 residues processed: 145 average time/residue: 0.1009 time to fit residues: 19.9955 Evaluate side-chains 143 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.2980 chunk 33 optimal weight: 20.0000 chunk 111 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 108 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS S 82 GLN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.173229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.139951 restraints weight = 9529.710| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.56 r_work: 0.3176 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8889 Z= 0.122 Angle : 0.483 8.671 12095 Z= 0.255 Chirality : 0.041 0.139 1403 Planarity : 0.003 0.035 1529 Dihedral : 4.884 53.441 1265 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.80 % Allowed : 25.67 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.54 (0.25), residues: 1133 helix: 1.75 (0.27), residues: 373 sheet: 0.01 (0.30), residues: 284 loop : -0.47 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 185 TYR 0.013 0.001 TYR S 178 PHE 0.014 0.001 PHE B 151 TRP 0.011 0.001 TRP B 169 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8885) covalent geometry : angle 0.48266 (12087) SS BOND : bond 0.00322 ( 4) SS BOND : angle 0.65483 ( 8) hydrogen bonds : bond 0.04487 ( 408) hydrogen bonds : angle 4.21315 ( 1149) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.348 Fit side-chains REVERT: B 338 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8454 (mp) REVERT: R 237 MET cc_start: 0.7176 (mtm) cc_final: 0.6799 (mtt) REVERT: R 279 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8161 (mm) REVERT: A 10 LYS cc_start: 0.8573 (ttmm) cc_final: 0.8236 (mttp) REVERT: A 21 LYS cc_start: 0.7795 (mmtp) cc_final: 0.7035 (ttpt) REVERT: S 39 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8350 (tt0) outliers start: 25 outliers final: 14 residues processed: 139 average time/residue: 0.0891 time to fit residues: 17.3491 Evaluate side-chains 134 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 72 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 111 optimal weight: 0.5980 chunk 98 optimal weight: 10.0000 chunk 67 optimal weight: 0.4980 chunk 1 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 108 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 0.3980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS S 82 GLN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.171205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.137840 restraints weight = 9775.766| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.62 r_work: 0.3184 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8889 Z= 0.108 Angle : 0.455 5.617 12095 Z= 0.242 Chirality : 0.040 0.135 1403 Planarity : 0.003 0.034 1529 Dihedral : 4.550 53.988 1265 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.81 % Allowed : 24.78 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.81 (0.25), residues: 1133 helix: 2.15 (0.27), residues: 373 sheet: 0.16 (0.30), residues: 281 loop : -0.47 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 18 TYR 0.012 0.001 TYR S 178 PHE 0.012 0.001 PHE B 151 TRP 0.010 0.001 TRP B 169 HIS 0.006 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 8885) covalent geometry : angle 0.45489 (12087) SS BOND : bond 0.00296 ( 4) SS BOND : angle 0.54058 ( 8) hydrogen bonds : bond 0.03945 ( 408) hydrogen bonds : angle 4.00296 ( 1149) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.305 Fit side-chains REVERT: B 338 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8458 (mp) REVERT: R 237 MET cc_start: 0.7184 (mtm) cc_final: 0.6850 (mtt) REVERT: R 279 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8203 (mm) REVERT: A 10 LYS cc_start: 0.8545 (ttmm) cc_final: 0.8211 (mttp) REVERT: A 21 LYS cc_start: 0.7845 (mttp) cc_final: 0.7103 (ttpt) REVERT: S 39 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8365 (tt0) outliers start: 34 outliers final: 20 residues processed: 139 average time/residue: 0.0972 time to fit residues: 18.6541 Evaluate side-chains 142 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 19 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 98 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS S 82 GLN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.162247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.126856 restraints weight = 9823.957| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.82 r_work: 0.3219 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8889 Z= 0.164 Angle : 0.514 7.223 12095 Z= 0.272 Chirality : 0.042 0.138 1403 Planarity : 0.003 0.037 1529 Dihedral : 4.861 53.682 1265 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.60 % Allowed : 24.55 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.79 (0.25), residues: 1133 helix: 2.16 (0.27), residues: 373 sheet: 0.12 (0.31), residues: 283 loop : -0.49 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 18 TYR 0.013 0.001 TYR S 103 PHE 0.017 0.001 PHE B 151 TRP 0.010 0.001 TRP B 169 HIS 0.007 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 8885) covalent geometry : angle 0.51384 (12087) SS BOND : bond 0.00357 ( 4) SS BOND : angle 0.69831 ( 8) hydrogen bonds : bond 0.04476 ( 408) hydrogen bonds : angle 4.14642 ( 1149) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 118 time to evaluate : 0.314 Fit side-chains REVERT: B 30 LEU cc_start: 0.6527 (OUTLIER) cc_final: 0.6271 (tt) REVERT: B 338 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8371 (mp) REVERT: R 189 ILE cc_start: 0.6542 (OUTLIER) cc_final: 0.6341 (pt) REVERT: R 237 MET cc_start: 0.7182 (mtm) cc_final: 0.6840 (mtt) REVERT: R 279 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8272 (mm) REVERT: R 318 MET cc_start: 0.7366 (tpp) cc_final: 0.7117 (tpp) REVERT: A 10 LYS cc_start: 0.8550 (ttmm) cc_final: 0.8188 (mttp) REVERT: A 21 LYS cc_start: 0.7952 (mttp) cc_final: 0.7263 (ttpt) REVERT: S 38 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8596 (ptt180) REVERT: S 39 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8365 (tt0) REVERT: S 175 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8472 (tp) outliers start: 41 outliers final: 25 residues processed: 146 average time/residue: 0.0892 time to fit residues: 18.4339 Evaluate side-chains 149 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 175 LEU Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 22 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 69 optimal weight: 0.5980 chunk 35 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 chunk 103 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS S 82 GLN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.161556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.125251 restraints weight = 9808.478| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.87 r_work: 0.3184 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8889 Z= 0.135 Angle : 0.483 6.573 12095 Z= 0.256 Chirality : 0.041 0.135 1403 Planarity : 0.003 0.036 1529 Dihedral : 4.766 54.520 1265 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.60 % Allowed : 25.00 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.89 (0.26), residues: 1133 helix: 2.32 (0.27), residues: 372 sheet: 0.17 (0.31), residues: 281 loop : -0.50 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 190 TYR 0.012 0.001 TYR S 178 PHE 0.015 0.001 PHE B 151 TRP 0.010 0.001 TRP B 169 HIS 0.007 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8885) covalent geometry : angle 0.48285 (12087) SS BOND : bond 0.00312 ( 4) SS BOND : angle 0.55342 ( 8) hydrogen bonds : bond 0.04096 ( 408) hydrogen bonds : angle 4.02794 ( 1149) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 0.358 Fit side-chains REVERT: B 338 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8360 (mp) REVERT: R 237 MET cc_start: 0.7166 (mtm) cc_final: 0.6842 (mtt) REVERT: R 279 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8253 (mm) REVERT: R 318 MET cc_start: 0.7452 (tpp) cc_final: 0.7110 (tpp) REVERT: A 10 LYS cc_start: 0.8534 (ttmm) cc_final: 0.8174 (mttp) REVERT: A 21 LYS cc_start: 0.7795 (mttp) cc_final: 0.7127 (ttpt) REVERT: S 38 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8579 (ptt180) REVERT: S 39 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8372 (tt0) REVERT: S 175 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8150 (tp) outliers start: 41 outliers final: 29 residues processed: 146 average time/residue: 0.0892 time to fit residues: 18.3671 Evaluate side-chains 153 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 145 GLU Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 175 LEU Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 98 optimal weight: 4.9990 chunk 0 optimal weight: 50.0000 chunk 80 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 59 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 85 optimal weight: 0.0070 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS S 82 GLN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.160321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.124291 restraints weight = 9974.915| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.99 r_work: 0.3207 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8889 Z= 0.100 Angle : 0.453 6.903 12095 Z= 0.239 Chirality : 0.040 0.130 1403 Planarity : 0.003 0.037 1529 Dihedral : 4.549 55.186 1265 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.70 % Allowed : 25.78 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.10 (0.26), residues: 1133 helix: 2.55 (0.27), residues: 372 sheet: 0.28 (0.31), residues: 280 loop : -0.41 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 18 TYR 0.012 0.001 TYR S 178 PHE 0.012 0.001 PHE B 151 TRP 0.010 0.001 TRP B 169 HIS 0.005 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 8885) covalent geometry : angle 0.45253 (12087) SS BOND : bond 0.00267 ( 4) SS BOND : angle 0.43179 ( 8) hydrogen bonds : bond 0.03599 ( 408) hydrogen bonds : angle 3.84713 ( 1149) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.324 Fit side-chains REVERT: B 338 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8422 (mp) REVERT: R 237 MET cc_start: 0.7146 (mtm) cc_final: 0.6848 (mtt) REVERT: R 279 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8218 (mm) REVERT: R 318 MET cc_start: 0.7340 (tpp) cc_final: 0.6987 (tpp) REVERT: A 10 LYS cc_start: 0.8492 (ttmm) cc_final: 0.8160 (mttp) REVERT: A 21 LYS cc_start: 0.7891 (mttp) cc_final: 0.7279 (ttpt) REVERT: S 39 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8345 (tt0) REVERT: S 175 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8135 (tp) outliers start: 33 outliers final: 24 residues processed: 146 average time/residue: 0.0920 time to fit residues: 18.8871 Evaluate side-chains 149 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 175 LEU Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 39 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 66 optimal weight: 0.0070 chunk 79 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 3 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 104 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 overall best weight: 1.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS S 82 GLN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.158429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.122889 restraints weight = 9898.822| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.96 r_work: 0.3200 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8889 Z= 0.117 Angle : 0.470 6.851 12095 Z= 0.248 Chirality : 0.041 0.135 1403 Planarity : 0.003 0.037 1529 Dihedral : 4.613 55.131 1265 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.81 % Allowed : 25.90 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.12 (0.26), residues: 1133 helix: 2.59 (0.27), residues: 372 sheet: 0.26 (0.31), residues: 281 loop : -0.42 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 18 TYR 0.012 0.001 TYR S 178 PHE 0.013 0.001 PHE B 151 TRP 0.009 0.001 TRP B 82 HIS 0.008 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8885) covalent geometry : angle 0.46955 (12087) SS BOND : bond 0.00292 ( 4) SS BOND : angle 0.52300 ( 8) hydrogen bonds : bond 0.03790 ( 408) hydrogen bonds : angle 3.87628 ( 1149) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 0.344 Fit side-chains REVERT: B 30 LEU cc_start: 0.6603 (OUTLIER) cc_final: 0.6309 (tt) REVERT: B 338 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8365 (mp) REVERT: R 237 MET cc_start: 0.7152 (mtm) cc_final: 0.6847 (mtt) REVERT: R 279 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8252 (mm) REVERT: R 318 MET cc_start: 0.7378 (tpp) cc_final: 0.6987 (tpp) REVERT: A 10 LYS cc_start: 0.8520 (ttmm) cc_final: 0.8173 (mttp) REVERT: A 21 LYS cc_start: 0.7877 (mttp) cc_final: 0.7243 (ttpt) REVERT: S 38 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8573 (ptt180) REVERT: S 39 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8343 (tt0) REVERT: S 175 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8127 (tp) outliers start: 34 outliers final: 24 residues processed: 145 average time/residue: 0.0940 time to fit residues: 18.9317 Evaluate side-chains 149 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 145 GLU Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 175 LEU Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 8 optimal weight: 0.1980 chunk 106 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.155652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.117703 restraints weight = 9863.851| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.85 r_work: 0.3247 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8889 Z= 0.192 Angle : 0.546 7.721 12095 Z= 0.287 Chirality : 0.044 0.184 1403 Planarity : 0.004 0.038 1529 Dihedral : 5.020 54.774 1265 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.37 % Allowed : 25.11 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.87 (0.26), residues: 1133 helix: 2.30 (0.27), residues: 374 sheet: 0.08 (0.31), residues: 283 loop : -0.46 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 18 TYR 0.014 0.002 TYR S 103 PHE 0.019 0.002 PHE B 151 TRP 0.010 0.001 TRP B 82 HIS 0.008 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 8885) covalent geometry : angle 0.54539 (12087) SS BOND : bond 0.00363 ( 4) SS BOND : angle 0.71213 ( 8) hydrogen bonds : bond 0.04542 ( 408) hydrogen bonds : angle 4.15701 ( 1149) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 116 time to evaluate : 0.325 Fit side-chains REVERT: B 30 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.6287 (tt) REVERT: B 338 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8400 (mp) REVERT: R 189 ILE cc_start: 0.6654 (OUTLIER) cc_final: 0.6435 (pt) REVERT: R 237 MET cc_start: 0.7395 (mtm) cc_final: 0.7024 (mtt) REVERT: R 275 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7165 (mp) REVERT: R 279 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8338 (mm) REVERT: R 318 MET cc_start: 0.7407 (tpp) cc_final: 0.6952 (tpp) REVERT: A 10 LYS cc_start: 0.8668 (ttmm) cc_final: 0.8307 (mttp) REVERT: A 21 LYS cc_start: 0.7972 (mttp) cc_final: 0.7311 (ttpt) REVERT: A 26 ASP cc_start: 0.7918 (p0) cc_final: 0.7635 (p0) REVERT: S 38 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8666 (ptt180) REVERT: S 39 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8448 (tt0) outliers start: 39 outliers final: 26 residues processed: 144 average time/residue: 0.0892 time to fit residues: 18.2882 Evaluate side-chains 149 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 103 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 2 optimal weight: 0.0070 chunk 86 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 99 optimal weight: 0.0770 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.159969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.124203 restraints weight = 9841.204| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.92 r_work: 0.3241 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8889 Z= 0.090 Angle : 0.456 7.203 12095 Z= 0.241 Chirality : 0.040 0.156 1403 Planarity : 0.003 0.038 1529 Dihedral : 4.585 56.495 1265 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.25 % Allowed : 26.12 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.15 (0.26), residues: 1133 helix: 2.65 (0.27), residues: 372 sheet: 0.29 (0.31), residues: 279 loop : -0.43 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 18 TYR 0.013 0.001 TYR S 178 PHE 0.010 0.001 PHE B 151 TRP 0.009 0.001 TRP B 169 HIS 0.015 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00199 ( 8885) covalent geometry : angle 0.45609 (12087) SS BOND : bond 0.00260 ( 4) SS BOND : angle 0.39529 ( 8) hydrogen bonds : bond 0.03504 ( 408) hydrogen bonds : angle 3.84614 ( 1149) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.326 Fit side-chains REVERT: B 30 LEU cc_start: 0.6613 (OUTLIER) cc_final: 0.6307 (tt) REVERT: B 338 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8430 (mp) REVERT: R 237 MET cc_start: 0.7177 (mtm) cc_final: 0.6875 (mtt) REVERT: R 275 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7118 (mp) REVERT: R 279 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8278 (mm) REVERT: R 318 MET cc_start: 0.7339 (tpp) cc_final: 0.6965 (tpp) REVERT: A 10 LYS cc_start: 0.8608 (ttmm) cc_final: 0.8272 (mttp) REVERT: A 21 LYS cc_start: 0.7917 (mttp) cc_final: 0.7235 (ttpt) REVERT: A 26 ASP cc_start: 0.7927 (p0) cc_final: 0.7615 (p0) REVERT: S 39 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8415 (tt0) REVERT: S 175 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8244 (tp) outliers start: 29 outliers final: 20 residues processed: 143 average time/residue: 0.0976 time to fit residues: 19.3145 Evaluate side-chains 143 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 175 LEU Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 70 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.158095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.122397 restraints weight = 9872.971| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.96 r_work: 0.3208 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8889 Z= 0.144 Angle : 0.506 7.113 12095 Z= 0.266 Chirality : 0.042 0.164 1403 Planarity : 0.003 0.038 1529 Dihedral : 4.794 56.001 1265 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.25 % Allowed : 26.12 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.07 (0.26), residues: 1133 helix: 2.57 (0.27), residues: 372 sheet: 0.14 (0.31), residues: 283 loop : -0.39 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 18 TYR 0.012 0.001 TYR S 103 PHE 0.015 0.001 PHE B 151 TRP 0.010 0.001 TRP B 82 HIS 0.018 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8885) covalent geometry : angle 0.50600 (12087) SS BOND : bond 0.00308 ( 4) SS BOND : angle 0.58765 ( 8) hydrogen bonds : bond 0.04060 ( 408) hydrogen bonds : angle 4.00617 ( 1149) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2259.85 seconds wall clock time: 39 minutes 27.04 seconds (2367.04 seconds total)