Starting phenix.real_space_refine on Wed Jun 3 23:11:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9upv_64403/06_2026/9upv_64403.cif Found real_map, /net/cci-nas-00/data/ceres_data/9upv_64403/06_2026/9upv_64403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9upv_64403/06_2026/9upv_64403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9upv_64403/06_2026/9upv_64403.map" model { file = "/net/cci-nas-00/data/ceres_data/9upv_64403/06_2026/9upv_64403.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9upv_64403/06_2026/9upv_64403.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5665 2.51 5 N 1480 2.21 5 O 1634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8837 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2516 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 4, 'GLU:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 345 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "J" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Classifications: {'peptide': 8} Link IDs: {'PTRANS': 1, 'TRANS': 6} Chain: "R" Number of atoms: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2296 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 9, 'TRANS': 275} Chain: "A" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1803 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.18, per 1000 atoms: 0.25 Number of scatterers: 8837 At special positions: 0 Unit cell: (90.95, 125.8, 130.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1634 8.00 N 1480 7.00 C 5665 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " 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 290.9 milliseconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 37.2% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 13 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.913A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.525A pdb=" N ASN C 59 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 66 Proline residue: R 42 - end of helix Processing helix chain 'R' and resid 71 through 89 removed outlier: 3.862A pdb=" N LYS R 75 " --> pdb=" O SER R 71 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR R 76 " --> pdb=" O MET R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 100 removed outlier: 3.641A pdb=" N TRP R 94 " --> pdb=" O THR R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 140 removed outlier: 4.021A pdb=" N VAL R 124 " --> pdb=" O LEU R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 154 removed outlier: 3.675A pdb=" N LYS R 149 " --> pdb=" O GLN R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 168 Processing helix chain 'R' and resid 168 through 174 Processing helix chain 'R' and resid 193 through 227 removed outlier: 3.920A pdb=" N VAL R 197 " --> pdb=" O ASP R 193 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU R 210 " --> pdb=" O VAL R 206 " (cutoff:3.500A) Proline residue: R 211 - end of helix removed outlier: 3.842A pdb=" N VAL R 214 " --> pdb=" O LEU R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 231 through 267 Proline residue: R 254 - end of helix Processing helix chain 'R' and resid 273 through 292 removed outlier: 4.119A pdb=" N GLU R 277 " --> pdb=" O GLY R 273 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN R 278 " --> pdb=" O CYS R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 303 Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 306 through 317 Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.581A pdb=" N LYS A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.514A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.306A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 327 through 351 removed outlier: 4.483A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.709A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 28 through 32' Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.140A 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 sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.636A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.768A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.839A 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: 7.043A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.596A 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 153 removed outlier: 6.729A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.764A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP B 212 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.752A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.964A 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: 3.959A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 177 through 180 Processing sheet with id=AA9, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.778A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.126A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.126A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 141 removed outlier: 3.546A pdb=" N VAL S 155 " --> pdb=" O ILE S 216 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA S 211 " --> pdb=" O SER S 208 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.854A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1203 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: 1.45 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: 1.21 - 1.34: 2589 1.34 - 1.46: 1794 1.46 - 1.58: 4568 1.58 - 1.70: 0 1.70 - 1.82: 81 Bond restraints: 9032 Sorted by residual: bond pdb=" CA LYS J 1 " pdb=" C LYS J 1 " ideal model delta sigma weight residual 1.525 1.448 0.077 2.10e-02 2.27e+03 1.33e+01 bond pdb=" N LYS J 1 " pdb=" CA LYS J 1 " ideal model delta sigma weight residual 1.458 1.423 0.035 1.90e-02 2.77e+03 3.31e+00 bond pdb=" C LYS J 1 " pdb=" N PRO J 2 " ideal model delta sigma weight residual 1.334 1.297 0.037 2.34e-02 1.83e+03 2.47e+00 bond pdb=" CA LEU J 5 " pdb=" C LEU J 5 " ideal model delta sigma weight residual 1.524 1.503 0.020 1.35e-02 5.49e+03 2.25e+00 bond pdb=" C LYS J 1 " pdb=" O LYS J 1 " ideal model delta sigma weight residual 1.231 1.214 0.017 2.00e-02 2.50e+03 7.34e-01 ... (remaining 9027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 12109 1.57 - 3.13: 114 3.13 - 4.70: 21 4.70 - 6.26: 5 6.26 - 7.83: 3 Bond angle restraints: 12252 Sorted by residual: angle pdb=" N LYS J 1 " pdb=" CA LYS J 1 " pdb=" C LYS J 1 " ideal model delta sigma weight residual 111.00 103.17 7.83 2.80e+00 1.28e-01 7.82e+00 angle pdb=" N LEU R 253 " pdb=" CA LEU R 253 " pdb=" C LEU R 253 " ideal model delta sigma weight residual 109.81 115.72 -5.91 2.21e+00 2.05e-01 7.16e+00 angle pdb=" N THR B 87 " pdb=" CA THR B 87 " pdb=" CB THR B 87 " ideal model delta sigma weight residual 113.65 110.03 3.62 1.47e+00 4.63e-01 6.07e+00 angle pdb=" C GLY R 207 " pdb=" N LEU R 208 " pdb=" CA LEU R 208 " ideal model delta sigma weight residual 122.15 115.80 6.35 2.83e+00 1.25e-01 5.04e+00 angle pdb=" N VAL R 158 " pdb=" CA VAL R 158 " pdb=" C VAL R 158 " ideal model delta sigma weight residual 109.34 113.21 -3.87 2.08e+00 2.31e-01 3.46e+00 ... (remaining 12247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.45: 4990 16.45 - 32.90: 324 32.90 - 49.35: 55 49.35 - 65.81: 3 65.81 - 82.26: 4 Dihedral angle restraints: 5376 sinusoidal: 2081 harmonic: 3295 Sorted by residual: dihedral pdb=" CA ARG S 191 " pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta harmonic sigma weight residual 180.00 163.01 16.99 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 164.15 15.85 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CB MET R 72 " pdb=" CG MET R 72 " pdb=" SD MET R 72 " pdb=" CE MET R 72 " ideal model delta sinusoidal sigma weight residual 180.00 124.58 55.42 3 1.50e+01 4.44e-03 9.35e+00 ... (remaining 5373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 835 0.026 - 0.051: 326 0.051 - 0.077: 142 0.077 - 0.102: 52 0.102 - 0.128: 46 Chirality restraints: 1401 Sorted by residual: chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA ILE C 25 " pdb=" N ILE C 25 " pdb=" C ILE C 25 " pdb=" CB ILE C 25 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 1398 not shown) Planarity restraints: 1534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO B 236 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 129 " -0.012 2.00e-02 2.50e+03 1.04e-02 1.88e+00 pdb=" CG PHE R 129 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE R 129 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE R 129 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE R 129 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE R 129 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE R 129 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 54 " -0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO C 55 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 55 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 55 " -0.019 5.00e-02 4.00e+02 ... (remaining 1531 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 553 2.74 - 3.28: 8240 3.28 - 3.82: 13499 3.82 - 4.36: 16016 4.36 - 4.90: 29566 Nonbonded interactions: 67874 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.198 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.218 3.040 nonbonded pdb=" O THR A 48 " pdb=" NE2 GLN A 52 " model vdw 2.258 3.120 nonbonded pdb=" O HIS R 140 " pdb=" OG SER R 144 " model vdw 2.286 3.040 nonbonded pdb=" OG SER A 263 " pdb=" O GLU A 318 " model vdw 2.313 3.040 ... (remaining 67869 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.030 Find NCS groups from input model: 0.040 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:6.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 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 : 0.002 0.077 9035 Z= 0.116 Angle : 0.445 7.830 12258 Z= 0.238 Chirality : 0.039 0.128 1401 Planarity : 0.003 0.042 1534 Dihedral : 11.214 82.256 3243 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: 1.14 (0.26), residues: 1119 helix: 2.77 (0.28), residues: 387 sheet: 0.51 (0.31), residues: 278 loop : -0.90 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 183 TYR 0.008 0.001 TYR S 235 PHE 0.024 0.001 PHE R 129 TRP 0.008 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 ( 9032) covalent geometry : angle 0.44439 / 0.24 (12252) SS BOND : bond 0.00333 / 0.16 ( 3) SS BOND : angle 1.20112 / 0.69 ( 6) hydrogen bonds : bond 0.16346 / 11.19 ( 418) hydrogen bonds : angle 5.79724 / 3.89 ( 1203) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: B 108 SER cc_start: 0.8283 (m) cc_final: 0.8060 (p) REVERT: B 155 ASN cc_start: 0.8113 (t0) cc_final: 0.7760 (t0) REVERT: B 254 ASP cc_start: 0.7877 (t70) cc_final: 0.7234 (t0) REVERT: B 258 ASP cc_start: 0.7405 (t0) cc_final: 0.7126 (t0) REVERT: B 280 LYS cc_start: 0.8478 (tttm) cc_final: 0.8236 (ttmm) REVERT: B 303 ASP cc_start: 0.7633 (m-30) cc_final: 0.7391 (m-30) REVERT: B 333 ASP cc_start: 0.7006 (t0) cc_final: 0.6731 (t0) REVERT: C 38 MET cc_start: 0.8102 (ttp) cc_final: 0.7828 (ttp) REVERT: R 50 LEU cc_start: 0.7723 (mt) cc_final: 0.7465 (mm) REVERT: R 154 LYS cc_start: 0.8134 (mmtm) cc_final: 0.7917 (mmtm) REVERT: R 229 SER cc_start: 0.8428 (m) cc_final: 0.8169 (t) REVERT: R 239 LYS cc_start: 0.7473 (ttpt) cc_final: 0.7232 (ttpt) REVERT: R 243 ILE cc_start: 0.7558 (mm) cc_final: 0.7331 (mt) REVERT: R 261 ILE cc_start: 0.7561 (mm) cc_final: 0.7341 (mt) REVERT: A 35 LYS cc_start: 0.8371 (mtmm) cc_final: 0.8050 (mtmm) REVERT: A 186 GLU cc_start: 0.8122 (tt0) cc_final: 0.7703 (tt0) REVERT: A 197 LYS cc_start: 0.8220 (mtmt) cc_final: 0.7815 (mtpp) REVERT: A 209 LYS cc_start: 0.8334 (pttt) cc_final: 0.7948 (tmtm) REVERT: A 216 GLU cc_start: 0.8157 (tt0) cc_final: 0.7927 (tt0) REVERT: A 275 GLU cc_start: 0.7860 (tp30) cc_final: 0.7548 (tp30) REVERT: A 279 LYS cc_start: 0.8290 (mtmt) cc_final: 0.8084 (mmtt) REVERT: A 298 GLU cc_start: 0.7346 (mt-10) cc_final: 0.7118 (mt-10) REVERT: A 314 LYS cc_start: 0.8379 (mttp) cc_final: 0.8163 (mmtt) REVERT: S 120 SER cc_start: 0.8001 (m) cc_final: 0.7671 (p) REVERT: S 139 VAL cc_start: 0.8691 (t) cc_final: 0.8390 (p) REVERT: S 204 SER cc_start: 0.8565 (m) cc_final: 0.8329 (t) REVERT: S 217 SER cc_start: 0.8335 (t) cc_final: 0.8009 (p) REVERT: S 234 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7161 (mp0) outliers start: 0 outliers final: 1 residues processed: 204 average time/residue: 0.6436 time to fit residues: 138.6955 Evaluate side-chains 170 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 169 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 259 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.0070 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 110 ASN B 175 GLN B 295 ASN R 66 GLN R 143 ASN R 315 HIS A 52 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN S 179 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.130914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.104968 restraints weight = 11984.299| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.48 r_work: 0.3274 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9035 Z= 0.126 Angle : 0.521 9.444 12258 Z= 0.270 Chirality : 0.041 0.150 1401 Planarity : 0.004 0.042 1534 Dihedral : 3.990 26.163 1286 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.79 % Allowed : 9.92 % Favored : 88.29 % 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: 1.20 (0.26), residues: 1119 helix: 2.72 (0.27), residues: 389 sheet: 0.59 (0.30), residues: 292 loop : -0.87 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 134 TYR 0.014 0.001 TYR S 190 PHE 0.011 0.001 PHE B 234 TRP 0.008 0.001 TRP S 36 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 9032) covalent geometry : angle 0.52074 / 0.27 (12252) SS BOND : bond 0.00664 / 0.32 ( 3) SS BOND : angle 1.13453 / 0.64 ( 6) hydrogen bonds : bond 0.05156 / 3.51 ( 418) hydrogen bonds : angle 4.31509 / 2.96 ( 1203) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 0.335 Fit side-chains REVERT: B 108 SER cc_start: 0.8256 (m) cc_final: 0.8037 (p) REVERT: B 155 ASN cc_start: 0.8106 (t0) cc_final: 0.7766 (t0) REVERT: B 214 ARG cc_start: 0.8172 (ttm170) cc_final: 0.7902 (ttm170) REVERT: B 217 MET cc_start: 0.8139 (ptt) cc_final: 0.7903 (ptt) REVERT: B 228 ASP cc_start: 0.8213 (m-30) cc_final: 0.7885 (m-30) REVERT: B 254 ASP cc_start: 0.7741 (t70) cc_final: 0.7270 (t0) REVERT: B 303 ASP cc_start: 0.7552 (m-30) cc_final: 0.7343 (m-30) REVERT: B 333 ASP cc_start: 0.6932 (t0) cc_final: 0.6628 (t0) REVERT: R 50 LEU cc_start: 0.7742 (mt) cc_final: 0.7495 (mm) REVERT: R 229 SER cc_start: 0.8386 (m) cc_final: 0.8054 (t) REVERT: R 239 LYS cc_start: 0.7411 (ttpt) cc_final: 0.7149 (ttpt) REVERT: R 243 ILE cc_start: 0.7454 (mm) cc_final: 0.7230 (mt) REVERT: R 261 ILE cc_start: 0.7202 (mm) cc_final: 0.7001 (mt) REVERT: A 20 ASP cc_start: 0.7261 (m-30) cc_final: 0.6887 (m-30) REVERT: A 25 GLU cc_start: 0.7235 (tm-30) cc_final: 0.6977 (tm-30) REVERT: A 33 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7390 (mt-10) REVERT: A 35 LYS cc_start: 0.8146 (mtmm) cc_final: 0.7879 (mtmm) REVERT: A 197 LYS cc_start: 0.8239 (mtmt) cc_final: 0.8026 (mtmm) REVERT: A 216 GLU cc_start: 0.8144 (tt0) cc_final: 0.7918 (tt0) REVERT: A 247 MET cc_start: 0.7303 (mtp) cc_final: 0.7008 (mtp) REVERT: A 275 GLU cc_start: 0.7974 (tp30) cc_final: 0.7600 (tp30) REVERT: A 279 LYS cc_start: 0.8340 (mtmt) cc_final: 0.8062 (mmtt) REVERT: A 294 ASN cc_start: 0.8023 (p0) cc_final: 0.7791 (p0) REVERT: A 298 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7193 (mt-10) REVERT: S 120 SER cc_start: 0.7997 (m) cc_final: 0.7659 (p) REVERT: S 139 VAL cc_start: 0.8616 (t) cc_final: 0.8309 (p) REVERT: S 158 SER cc_start: 0.8878 (p) cc_final: 0.8453 (t) REVERT: S 204 SER cc_start: 0.7940 (m) cc_final: 0.7708 (t) REVERT: S 217 SER cc_start: 0.8499 (t) cc_final: 0.8146 (p) REVERT: S 218 ARG cc_start: 0.7863 (ttp80) cc_final: 0.7628 (tpp80) REVERT: S 223 ASP cc_start: 0.8105 (m-30) cc_final: 0.7840 (m-30) REVERT: S 234 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7269 (mp0) outliers start: 17 outliers final: 1 residues processed: 185 average time/residue: 0.6608 time to fit residues: 128.8954 Evaluate side-chains 160 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 109 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 GLN R 143 ASN R 315 HIS A 188 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.129722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.103386 restraints weight = 11858.956| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.47 r_work: 0.3230 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9035 Z= 0.171 Angle : 0.526 6.925 12258 Z= 0.277 Chirality : 0.042 0.155 1401 Planarity : 0.004 0.044 1534 Dihedral : 4.064 24.732 1284 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.00 % Allowed : 11.39 % Favored : 86.60 % 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: 1.06 (0.26), residues: 1119 helix: 2.64 (0.27), residues: 386 sheet: 0.46 (0.29), residues: 305 loop : -0.95 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.016 0.001 TYR B 105 PHE 0.020 0.002 PHE R 36 TRP 0.010 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 ( 9032) covalent geometry : angle 0.52574 / 0.28 (12252) SS BOND : bond 0.00712 / 0.35 ( 3) SS BOND : angle 1.32160 / 0.75 ( 6) hydrogen bonds : bond 0.05798 / 3.97 ( 418) hydrogen bonds : angle 4.22685 / 2.91 ( 1203) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.353 Fit side-chains REVERT: B 108 SER cc_start: 0.8372 (m) cc_final: 0.8130 (p) REVERT: B 155 ASN cc_start: 0.8202 (t0) cc_final: 0.7843 (t0) REVERT: B 214 ARG cc_start: 0.8406 (ttm170) cc_final: 0.8115 (ttm170) REVERT: B 228 ASP cc_start: 0.8442 (m-30) cc_final: 0.8091 (m-30) REVERT: B 254 ASP cc_start: 0.8048 (t70) cc_final: 0.7552 (t0) REVERT: B 333 ASP cc_start: 0.7201 (t0) cc_final: 0.6881 (t0) REVERT: R 50 LEU cc_start: 0.7830 (mt) cc_final: 0.7589 (mm) REVERT: R 171 ASP cc_start: 0.5875 (m-30) cc_final: 0.5665 (m-30) REVERT: R 229 SER cc_start: 0.8433 (m) cc_final: 0.8061 (t) REVERT: R 239 LYS cc_start: 0.7798 (ttpt) cc_final: 0.7511 (ttpt) REVERT: R 243 ILE cc_start: 0.7549 (mm) cc_final: 0.7345 (mt) REVERT: R 261 ILE cc_start: 0.7522 (mm) cc_final: 0.7319 (mt) REVERT: R 296 CYS cc_start: 0.7654 (m) cc_final: 0.7447 (m) REVERT: A 25 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7161 (tp30) REVERT: A 26 ASP cc_start: 0.7559 (m-30) cc_final: 0.7356 (t0) REVERT: A 33 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7712 (mt-10) REVERT: A 193 ASP cc_start: 0.8258 (m-30) cc_final: 0.7845 (p0) REVERT: A 197 LYS cc_start: 0.8440 (mtmt) cc_final: 0.8160 (mtmm) REVERT: A 207 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7259 (tt0) REVERT: A 279 LYS cc_start: 0.8350 (mtmt) cc_final: 0.8095 (mmtt) REVERT: A 294 ASN cc_start: 0.8082 (p0) cc_final: 0.7833 (p0) REVERT: A 312 LYS cc_start: 0.8416 (mmtm) cc_final: 0.8156 (mmtt) REVERT: S 39 GLN cc_start: 0.8667 (pt0) cc_final: 0.8354 (tt0) REVERT: S 43 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7961 (mmmm) REVERT: S 120 SER cc_start: 0.8090 (m) cc_final: 0.7746 (p) REVERT: S 139 VAL cc_start: 0.8682 (t) cc_final: 0.8347 (p) REVERT: S 158 SER cc_start: 0.8935 (p) cc_final: 0.8520 (t) REVERT: S 217 SER cc_start: 0.8489 (t) cc_final: 0.8153 (p) REVERT: S 218 ARG cc_start: 0.8107 (ttp80) cc_final: 0.7860 (tpp80) REVERT: S 223 ASP cc_start: 0.8177 (m-30) cc_final: 0.7937 (m-30) REVERT: S 234 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7519 (mp0) outliers start: 19 outliers final: 6 residues processed: 164 average time/residue: 0.6698 time to fit residues: 115.9208 Evaluate side-chains 165 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 158 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain S residue 43 LYS Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 88 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 20 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 84 optimal weight: 0.0980 chunk 4 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 143 ASN R 315 HIS A 195 HIS A 322 HIS A 331 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.131088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.104314 restraints weight = 11872.813| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.53 r_work: 0.3249 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9035 Z= 0.130 Angle : 0.509 8.148 12258 Z= 0.264 Chirality : 0.041 0.143 1401 Planarity : 0.004 0.044 1534 Dihedral : 3.956 23.069 1284 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.22 % Allowed : 12.45 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.26), residues: 1119 helix: 2.71 (0.27), residues: 386 sheet: 0.46 (0.30), residues: 302 loop : -0.93 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 134 TYR 0.013 0.001 TYR S 190 PHE 0.022 0.001 PHE R 36 TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 9032) covalent geometry : angle 0.50826 / 0.26 (12252) SS BOND : bond 0.00585 / 0.29 ( 3) SS BOND : angle 1.22803 / 0.70 ( 6) hydrogen bonds : bond 0.05058 / 3.47 ( 418) hydrogen bonds : angle 4.08339 / 2.82 ( 1203) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: B 108 SER cc_start: 0.8274 (m) cc_final: 0.8030 (p) REVERT: B 155 ASN cc_start: 0.8067 (t0) cc_final: 0.7740 (t0) REVERT: B 214 ARG cc_start: 0.8149 (ttm170) cc_final: 0.7863 (ttm170) REVERT: B 228 ASP cc_start: 0.8222 (m-30) cc_final: 0.7841 (m-30) REVERT: B 254 ASP cc_start: 0.7776 (t70) cc_final: 0.7313 (t0) REVERT: B 333 ASP cc_start: 0.6893 (t0) cc_final: 0.6603 (t0) REVERT: R 50 LEU cc_start: 0.7663 (mt) cc_final: 0.7414 (mm) REVERT: R 171 ASP cc_start: 0.5648 (m-30) cc_final: 0.5404 (m-30) REVERT: R 172 PHE cc_start: 0.7733 (OUTLIER) cc_final: 0.7304 (m-80) REVERT: R 229 SER cc_start: 0.8390 (m) cc_final: 0.8060 (t) REVERT: R 239 LYS cc_start: 0.7419 (ttpt) cc_final: 0.7141 (ttpt) REVERT: R 243 ILE cc_start: 0.7401 (mm) cc_final: 0.7177 (mt) REVERT: R 261 ILE cc_start: 0.7162 (mm) cc_final: 0.6951 (mt) REVERT: A 20 ASP cc_start: 0.7308 (m-30) cc_final: 0.6915 (m-30) REVERT: A 25 GLU cc_start: 0.7231 (tm-30) cc_final: 0.6948 (tp30) REVERT: A 33 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7483 (mt-10) REVERT: A 51 LYS cc_start: 0.8147 (tmmm) cc_final: 0.7944 (tmmt) REVERT: A 197 LYS cc_start: 0.8209 (mtmt) cc_final: 0.7979 (mtmm) REVERT: A 207 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7033 (tt0) REVERT: A 247 MET cc_start: 0.7235 (mtp) cc_final: 0.6923 (mtp) REVERT: A 279 LYS cc_start: 0.8319 (mtmt) cc_final: 0.8065 (mmtt) REVERT: A 294 ASN cc_start: 0.8029 (p0) cc_final: 0.7782 (p0) REVERT: A 297 GLU cc_start: 0.7312 (tp30) cc_final: 0.7096 (tp30) REVERT: S 39 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8194 (tt0) REVERT: S 120 SER cc_start: 0.7986 (m) cc_final: 0.7677 (p) REVERT: S 139 VAL cc_start: 0.8646 (t) cc_final: 0.8339 (p) REVERT: S 158 SER cc_start: 0.8914 (p) cc_final: 0.8507 (t) REVERT: S 217 SER cc_start: 0.8466 (t) cc_final: 0.8136 (p) REVERT: S 218 ARG cc_start: 0.7900 (ttp80) cc_final: 0.7690 (tpp80) REVERT: S 223 ASP cc_start: 0.8056 (m-30) cc_final: 0.7832 (m-30) REVERT: S 234 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7276 (mp0) outliers start: 21 outliers final: 9 residues processed: 170 average time/residue: 0.6497 time to fit residues: 116.7350 Evaluate side-chains 163 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain R residue 40 PHE Chi-restraints excluded: chain R residue 172 PHE Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 314 GLN Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 88 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 77 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 19 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 107 optimal weight: 0.0980 chunk 110 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 143 ASN R 315 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.131050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.103671 restraints weight = 11954.351| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.62 r_work: 0.3257 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9035 Z= 0.110 Angle : 0.495 9.387 12258 Z= 0.255 Chirality : 0.040 0.129 1401 Planarity : 0.003 0.042 1534 Dihedral : 3.829 22.188 1284 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.64 % Allowed : 12.76 % Favored : 84.60 % 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: 1.16 (0.26), residues: 1119 helix: 2.79 (0.27), residues: 385 sheet: 0.46 (0.30), residues: 302 loop : -0.91 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.013 0.001 TYR S 190 PHE 0.017 0.001 PHE R 174 TRP 0.008 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 9032) covalent geometry : angle 0.49440 / 0.25 (12252) SS BOND : bond 0.00517 / 0.25 ( 3) SS BOND : angle 1.18273 / 0.67 ( 6) hydrogen bonds : bond 0.04558 / 3.13 ( 418) hydrogen bonds : angle 3.94934 / 2.73 ( 1203) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 SER cc_start: 0.8243 (m) cc_final: 0.7971 (p) REVERT: B 155 ASN cc_start: 0.8029 (t0) cc_final: 0.7684 (t0) REVERT: B 214 ARG cc_start: 0.8169 (ttm170) cc_final: 0.7857 (ttm170) REVERT: B 228 ASP cc_start: 0.8222 (m-30) cc_final: 0.7809 (m-30) REVERT: B 234 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.8249 (m-80) REVERT: B 254 ASP cc_start: 0.7773 (t70) cc_final: 0.7258 (t0) REVERT: R 50 LEU cc_start: 0.7542 (mt) cc_final: 0.7287 (mm) REVERT: R 171 ASP cc_start: 0.5640 (m-30) cc_final: 0.5386 (m-30) REVERT: R 229 SER cc_start: 0.8312 (m) cc_final: 0.7984 (t) REVERT: R 243 ILE cc_start: 0.7291 (mm) cc_final: 0.7058 (mt) REVERT: R 261 ILE cc_start: 0.7061 (mm) cc_final: 0.6846 (mt) REVERT: A 25 GLU cc_start: 0.7094 (tm-30) cc_final: 0.6788 (tp30) REVERT: A 33 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7376 (mt-10) REVERT: A 193 ASP cc_start: 0.8059 (m-30) cc_final: 0.7697 (p0) REVERT: A 197 LYS cc_start: 0.8183 (mtmt) cc_final: 0.7929 (mtmm) REVERT: A 207 GLU cc_start: 0.7526 (mt-10) cc_final: 0.6971 (tt0) REVERT: A 247 MET cc_start: 0.7194 (mtp) cc_final: 0.6831 (mtp) REVERT: A 279 LYS cc_start: 0.8308 (mtmt) cc_final: 0.8054 (mmtt) REVERT: A 294 ASN cc_start: 0.7991 (p0) cc_final: 0.7754 (p0) REVERT: A 297 GLU cc_start: 0.7291 (tp30) cc_final: 0.7059 (tp30) REVERT: S 39 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8065 (tt0) REVERT: S 43 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7865 (mmmm) REVERT: S 120 SER cc_start: 0.7973 (m) cc_final: 0.7641 (p) REVERT: S 139 VAL cc_start: 0.8622 (t) cc_final: 0.8303 (p) REVERT: S 158 SER cc_start: 0.8901 (p) cc_final: 0.8487 (t) REVERT: S 217 SER cc_start: 0.8422 (t) cc_final: 0.8068 (p) REVERT: S 218 ARG cc_start: 0.7986 (ttp80) cc_final: 0.7743 (tpp80) REVERT: S 223 ASP cc_start: 0.8030 (m-30) cc_final: 0.7765 (m-30) REVERT: S 234 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7229 (mp0) outliers start: 25 outliers final: 12 residues processed: 163 average time/residue: 0.6483 time to fit residues: 111.7721 Evaluate side-chains 174 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain R residue 40 PHE Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 314 GLN Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 43 LYS Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 192 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 54 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 143 ASN R 315 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.130769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.104243 restraints weight = 11901.165| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.52 r_work: 0.3258 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9035 Z= 0.128 Angle : 0.521 10.459 12258 Z= 0.266 Chirality : 0.041 0.139 1401 Planarity : 0.004 0.042 1534 Dihedral : 3.854 21.731 1284 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.64 % Allowed : 14.35 % Favored : 83.02 % 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: 1.12 (0.26), residues: 1119 helix: 2.76 (0.27), residues: 386 sheet: 0.45 (0.30), residues: 303 loop : -0.96 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 134 TYR 0.013 0.001 TYR S 190 PHE 0.017 0.001 PHE R 174 TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 9032) covalent geometry : angle 0.52050 / 0.27 (12252) SS BOND : bond 0.00548 / 0.27 ( 3) SS BOND : angle 1.25641 / 0.71 ( 6) hydrogen bonds : bond 0.04813 / 3.31 ( 418) hydrogen bonds : angle 3.93705 / 2.72 ( 1203) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 SER cc_start: 0.8287 (m) cc_final: 0.8040 (p) REVERT: B 155 ASN cc_start: 0.8048 (t0) cc_final: 0.7731 (t0) REVERT: B 214 ARG cc_start: 0.8154 (ttm170) cc_final: 0.7849 (ttm170) REVERT: B 228 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7767 (m-30) REVERT: B 254 ASP cc_start: 0.7764 (t70) cc_final: 0.7306 (t0) REVERT: R 50 LEU cc_start: 0.7657 (mt) cc_final: 0.7402 (mm) REVERT: R 171 ASP cc_start: 0.5530 (m-30) cc_final: 0.5299 (m-30) REVERT: R 229 SER cc_start: 0.8321 (m) cc_final: 0.8002 (t) REVERT: R 243 ILE cc_start: 0.7447 (mm) cc_final: 0.7222 (mt) REVERT: R 261 ILE cc_start: 0.7181 (mm) cc_final: 0.6965 (mt) REVERT: A 20 ASP cc_start: 0.7332 (m-30) cc_final: 0.6953 (m-30) REVERT: A 25 GLU cc_start: 0.7228 (tm-30) cc_final: 0.6930 (tp30) REVERT: A 33 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7352 (mt-10) REVERT: A 197 LYS cc_start: 0.8212 (mtmt) cc_final: 0.7995 (mtmm) REVERT: A 207 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7050 (tt0) REVERT: A 279 LYS cc_start: 0.8328 (mtmt) cc_final: 0.8080 (mmtt) REVERT: A 294 ASN cc_start: 0.8013 (p0) cc_final: 0.7797 (p0) REVERT: A 297 GLU cc_start: 0.7344 (tp30) cc_final: 0.7099 (tp30) REVERT: S 39 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8156 (tt0) REVERT: S 43 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7959 (mmmm) REVERT: S 120 SER cc_start: 0.7998 (m) cc_final: 0.7696 (p) REVERT: S 139 VAL cc_start: 0.8678 (t) cc_final: 0.8370 (p) REVERT: S 158 SER cc_start: 0.8894 (p) cc_final: 0.8487 (t) REVERT: S 217 SER cc_start: 0.8463 (t) cc_final: 0.8112 (p) REVERT: S 218 ARG cc_start: 0.7993 (ttp80) cc_final: 0.7771 (tpp80) REVERT: S 223 ASP cc_start: 0.8071 (m-30) cc_final: 0.7823 (m-30) REVERT: S 234 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7319 (mp0) outliers start: 25 outliers final: 11 residues processed: 165 average time/residue: 0.6359 time to fit residues: 111.2216 Evaluate side-chains 158 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain R residue 40 PHE Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 43 LYS Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 192 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 64 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 HIS R 143 ASN R 315 HIS A 52 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.129844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.103532 restraints weight = 12058.842| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.51 r_work: 0.3249 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9035 Z= 0.139 Angle : 0.539 11.149 12258 Z= 0.275 Chirality : 0.041 0.141 1401 Planarity : 0.004 0.075 1534 Dihedral : 3.899 21.274 1284 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.95 % Allowed : 14.24 % Favored : 82.81 % 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: 1.12 (0.26), residues: 1119 helix: 2.76 (0.27), residues: 386 sheet: 0.43 (0.30), residues: 302 loop : -0.93 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 134 TYR 0.013 0.001 TYR S 190 PHE 0.016 0.001 PHE R 174 TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 9032) covalent geometry : angle 0.53861 / 0.28 (12252) SS BOND : bond 0.00583 / 0.28 ( 3) SS BOND : angle 1.32461 / 0.75 ( 6) hydrogen bonds : bond 0.05010 / 3.44 ( 418) hydrogen bonds : angle 3.95652 / 2.74 ( 1203) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: B 108 SER cc_start: 0.8300 (m) cc_final: 0.8046 (p) REVERT: B 155 ASN cc_start: 0.8053 (t0) cc_final: 0.7744 (t0) REVERT: B 214 ARG cc_start: 0.8167 (ttm170) cc_final: 0.7867 (ttm170) REVERT: B 228 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7828 (m-30) REVERT: B 254 ASP cc_start: 0.7766 (t70) cc_final: 0.7304 (t0) REVERT: R 50 LEU cc_start: 0.7665 (mt) cc_final: 0.7421 (mm) REVERT: R 171 ASP cc_start: 0.5500 (m-30) cc_final: 0.5266 (m-30) REVERT: R 229 SER cc_start: 0.8347 (m) cc_final: 0.8020 (t) REVERT: R 239 LYS cc_start: 0.7457 (ttpt) cc_final: 0.7172 (ttpt) REVERT: R 243 ILE cc_start: 0.7425 (mm) cc_final: 0.7193 (mt) REVERT: R 261 ILE cc_start: 0.7202 (mm) cc_final: 0.6988 (mt) REVERT: A 25 GLU cc_start: 0.7225 (tm-30) cc_final: 0.6912 (tp30) REVERT: A 33 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7344 (mt-10) REVERT: A 52 GLN cc_start: 0.7139 (OUTLIER) cc_final: 0.6920 (mp10) REVERT: A 193 ASP cc_start: 0.8014 (m-30) cc_final: 0.7717 (p0) REVERT: A 197 LYS cc_start: 0.8211 (mtmt) cc_final: 0.7994 (mtmm) REVERT: A 207 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7043 (tt0) REVERT: A 247 MET cc_start: 0.7346 (mtp) cc_final: 0.7097 (mtp) REVERT: A 279 LYS cc_start: 0.8281 (mtmt) cc_final: 0.8068 (mmtt) REVERT: A 297 GLU cc_start: 0.7372 (tp30) cc_final: 0.7125 (tp30) REVERT: A 312 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7763 (mmtm) REVERT: S 39 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8191 (tt0) REVERT: S 43 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7985 (mmmm) REVERT: S 120 SER cc_start: 0.8001 (m) cc_final: 0.7707 (p) REVERT: S 139 VAL cc_start: 0.8662 (t) cc_final: 0.8354 (p) REVERT: S 158 SER cc_start: 0.8909 (p) cc_final: 0.8497 (t) REVERT: S 160 ARG cc_start: 0.7264 (ttp-110) cc_final: 0.6962 (ttp-110) REVERT: S 217 SER cc_start: 0.8462 (t) cc_final: 0.8114 (p) REVERT: S 218 ARG cc_start: 0.7988 (ttp80) cc_final: 0.7781 (tpp80) REVERT: S 223 ASP cc_start: 0.8082 (m-30) cc_final: 0.7816 (m-30) REVERT: S 234 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7334 (mp0) outliers start: 28 outliers final: 14 residues processed: 165 average time/residue: 0.6712 time to fit residues: 116.9635 Evaluate side-chains 174 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 40 PHE Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 314 GLN Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 43 LYS Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 192 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 37 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 29 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 HIS R 143 ASN A 52 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.130365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.104314 restraints weight = 11942.471| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.47 r_work: 0.3253 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9035 Z= 0.128 Angle : 0.541 11.616 12258 Z= 0.275 Chirality : 0.041 0.138 1401 Planarity : 0.004 0.052 1534 Dihedral : 3.874 20.964 1284 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.64 % Allowed : 15.51 % Favored : 81.86 % 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: 1.17 (0.26), residues: 1119 helix: 2.80 (0.27), residues: 386 sheet: 0.51 (0.30), residues: 305 loop : -0.95 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 134 TYR 0.013 0.001 TYR S 190 PHE 0.016 0.001 PHE R 174 TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 9032) covalent geometry : angle 0.54048 / 0.27 (12252) SS BOND : bond 0.00559 / 0.27 ( 3) SS BOND : angle 1.29583 / 0.73 ( 6) hydrogen bonds : bond 0.04859 / 3.34 ( 418) hydrogen bonds : angle 3.94021 / 2.73 ( 1203) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: B 108 SER cc_start: 0.8306 (m) cc_final: 0.8057 (p) REVERT: B 155 ASN cc_start: 0.8047 (t0) cc_final: 0.7748 (t0) REVERT: B 214 ARG cc_start: 0.8148 (ttm170) cc_final: 0.7847 (ttm170) REVERT: B 254 ASP cc_start: 0.7732 (t70) cc_final: 0.7287 (t0) REVERT: R 50 LEU cc_start: 0.7701 (mt) cc_final: 0.7448 (mm) REVERT: R 171 ASP cc_start: 0.5489 (m-30) cc_final: 0.5256 (m-30) REVERT: R 172 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.7183 (m-10) REVERT: R 229 SER cc_start: 0.8347 (m) cc_final: 0.8037 (t) REVERT: R 243 ILE cc_start: 0.7440 (mm) cc_final: 0.7214 (mt) REVERT: R 261 ILE cc_start: 0.7214 (mm) cc_final: 0.6998 (mt) REVERT: A 20 ASP cc_start: 0.7343 (m-30) cc_final: 0.6965 (m-30) REVERT: A 25 GLU cc_start: 0.7222 (tm-30) cc_final: 0.6924 (tp30) REVERT: A 33 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7341 (mt-10) REVERT: A 197 LYS cc_start: 0.8217 (mtmt) cc_final: 0.8004 (mtmm) REVERT: A 207 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7024 (tt0) REVERT: A 279 LYS cc_start: 0.8271 (mtmt) cc_final: 0.8064 (mmtt) REVERT: A 297 GLU cc_start: 0.7376 (tp30) cc_final: 0.7116 (tp30) REVERT: A 312 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7761 (mmtm) REVERT: S 39 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8078 (tt0) REVERT: S 43 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7901 (mmmm) REVERT: S 120 SER cc_start: 0.7998 (m) cc_final: 0.7709 (p) REVERT: S 139 VAL cc_start: 0.8681 (t) cc_final: 0.8382 (p) REVERT: S 158 SER cc_start: 0.8901 (p) cc_final: 0.8493 (t) REVERT: S 160 ARG cc_start: 0.7260 (ttp-110) cc_final: 0.6966 (ttp-110) REVERT: S 217 SER cc_start: 0.8474 (t) cc_final: 0.8127 (p) REVERT: S 223 ASP cc_start: 0.8068 (m-30) cc_final: 0.7811 (m-30) REVERT: S 234 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7312 (mp0) outliers start: 25 outliers final: 15 residues processed: 169 average time/residue: 0.6093 time to fit residues: 109.2371 Evaluate side-chains 165 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 40 PHE Chi-restraints excluded: chain R residue 172 PHE Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 314 GLN Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 43 LYS Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 192 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 chunk 101 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 47 optimal weight: 0.0870 chunk 50 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 HIS ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.130360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.103790 restraints weight = 11870.807| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.52 r_work: 0.3249 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9035 Z= 0.133 Angle : 0.557 11.760 12258 Z= 0.284 Chirality : 0.041 0.138 1401 Planarity : 0.004 0.084 1534 Dihedral : 3.879 20.678 1284 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.11 % Allowed : 16.35 % Favored : 81.54 % 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: 1.17 (0.26), residues: 1119 helix: 2.78 (0.27), residues: 387 sheet: 0.51 (0.30), residues: 305 loop : -0.95 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 134 TYR 0.013 0.001 TYR S 190 PHE 0.016 0.001 PHE R 174 TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 9032) covalent geometry : angle 0.55653 / 0.28 (12252) SS BOND : bond 0.00561 / 0.27 ( 3) SS BOND : angle 1.30183 / 0.73 ( 6) hydrogen bonds : bond 0.04878 / 3.36 ( 418) hydrogen bonds : angle 3.94503 / 2.73 ( 1203) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: B 108 SER cc_start: 0.8356 (m) cc_final: 0.8105 (p) REVERT: B 155 ASN cc_start: 0.8029 (t0) cc_final: 0.7728 (t0) REVERT: B 214 ARG cc_start: 0.8154 (ttm170) cc_final: 0.7847 (ttm170) REVERT: B 219 ARG cc_start: 0.7711 (mmm-85) cc_final: 0.7466 (mmm-85) REVERT: B 254 ASP cc_start: 0.7740 (t70) cc_final: 0.7276 (t0) REVERT: R 50 LEU cc_start: 0.7680 (mt) cc_final: 0.7430 (mm) REVERT: R 171 ASP cc_start: 0.5476 (m-30) cc_final: 0.5240 (m-30) REVERT: R 172 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.7139 (m-80) REVERT: R 229 SER cc_start: 0.8333 (m) cc_final: 0.8021 (t) REVERT: R 243 ILE cc_start: 0.7413 (mm) cc_final: 0.7179 (mt) REVERT: R 261 ILE cc_start: 0.7187 (mm) cc_final: 0.6971 (mt) REVERT: A 25 GLU cc_start: 0.7203 (tm-30) cc_final: 0.6915 (tp30) REVERT: A 33 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7351 (mt-10) REVERT: A 193 ASP cc_start: 0.7998 (m-30) cc_final: 0.7697 (p0) REVERT: A 197 LYS cc_start: 0.8213 (mtmt) cc_final: 0.7988 (mtmm) REVERT: A 207 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7019 (tt0) REVERT: A 247 MET cc_start: 0.7345 (mtp) cc_final: 0.7106 (mtp) REVERT: A 279 LYS cc_start: 0.8260 (mtmt) cc_final: 0.8044 (mmtt) REVERT: A 297 GLU cc_start: 0.7369 (tp30) cc_final: 0.7101 (tp30) REVERT: A 312 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7760 (mmtm) REVERT: S 39 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8068 (tt0) REVERT: S 43 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7881 (mmmm) REVERT: S 120 SER cc_start: 0.7989 (m) cc_final: 0.7698 (p) REVERT: S 139 VAL cc_start: 0.8668 (t) cc_final: 0.8367 (p) REVERT: S 158 SER cc_start: 0.8898 (p) cc_final: 0.8486 (t) REVERT: S 160 ARG cc_start: 0.7260 (ttp-110) cc_final: 0.6965 (ttp-110) REVERT: S 217 SER cc_start: 0.8478 (t) cc_final: 0.8142 (p) REVERT: S 223 ASP cc_start: 0.8105 (m-30) cc_final: 0.7880 (m-30) REVERT: S 234 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7308 (mp0) outliers start: 20 outliers final: 12 residues processed: 158 average time/residue: 0.6397 time to fit residues: 107.1141 Evaluate side-chains 168 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 40 PHE Chi-restraints excluded: chain R residue 172 PHE Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 314 GLN Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 43 LYS Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 88 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 71 optimal weight: 0.3980 chunk 88 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 HIS ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.130338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.103647 restraints weight = 11961.537| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.53 r_work: 0.3249 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9035 Z= 0.133 Angle : 0.559 12.358 12258 Z= 0.284 Chirality : 0.041 0.138 1401 Planarity : 0.004 0.061 1534 Dihedral : 3.863 20.293 1284 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.90 % Allowed : 16.77 % Favored : 81.33 % 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: 1.18 (0.26), residues: 1119 helix: 2.79 (0.27), residues: 387 sheet: 0.53 (0.30), residues: 305 loop : -0.95 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 134 TYR 0.013 0.001 TYR S 190 PHE 0.031 0.001 PHE R 36 TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 9032) covalent geometry : angle 0.55854 / 0.28 (12252) SS BOND : bond 0.00576 / 0.28 ( 3) SS BOND : angle 1.31082 / 0.73 ( 6) hydrogen bonds : bond 0.04863 / 3.34 ( 418) hydrogen bonds : angle 3.94453 / 2.73 ( 1203) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: B 108 SER cc_start: 0.8376 (m) cc_final: 0.8123 (p) REVERT: B 155 ASN cc_start: 0.8035 (t0) cc_final: 0.7719 (t0) REVERT: B 214 ARG cc_start: 0.8173 (ttm170) cc_final: 0.7866 (ttm170) REVERT: B 219 ARG cc_start: 0.7721 (mmm-85) cc_final: 0.7494 (mmm-85) REVERT: B 254 ASP cc_start: 0.7746 (t70) cc_final: 0.7286 (t0) REVERT: R 50 LEU cc_start: 0.7682 (mt) cc_final: 0.7434 (mm) REVERT: R 171 ASP cc_start: 0.5430 (m-30) cc_final: 0.5197 (m-30) REVERT: R 172 PHE cc_start: 0.7647 (OUTLIER) cc_final: 0.7140 (m-10) REVERT: R 243 ILE cc_start: 0.7414 (mm) cc_final: 0.7180 (mt) REVERT: R 261 ILE cc_start: 0.7198 (mm) cc_final: 0.6981 (mt) REVERT: A 20 ASP cc_start: 0.7337 (m-30) cc_final: 0.6955 (m-30) REVERT: A 33 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7370 (mt-10) REVERT: A 197 LYS cc_start: 0.8217 (mtmt) cc_final: 0.7990 (mtmm) REVERT: A 207 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7010 (tt0) REVERT: A 276 GLU cc_start: 0.7474 (tp30) cc_final: 0.7107 (tp30) REVERT: A 297 GLU cc_start: 0.7392 (tp30) cc_final: 0.7079 (tp30) REVERT: S 39 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8066 (tt0) REVERT: S 43 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7899 (mmmm) REVERT: S 120 SER cc_start: 0.7991 (m) cc_final: 0.7701 (p) REVERT: S 139 VAL cc_start: 0.8683 (t) cc_final: 0.8383 (p) REVERT: S 158 SER cc_start: 0.8901 (p) cc_final: 0.8488 (t) REVERT: S 160 ARG cc_start: 0.7253 (ttp-110) cc_final: 0.6976 (ttp-110) REVERT: S 217 SER cc_start: 0.8521 (t) cc_final: 0.7990 (p) REVERT: S 223 ASP cc_start: 0.8110 (m-30) cc_final: 0.7794 (m-30) REVERT: S 234 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7302 (mp0) outliers start: 18 outliers final: 11 residues processed: 162 average time/residue: 0.6390 time to fit residues: 109.9015 Evaluate side-chains 157 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 40 PHE Chi-restraints excluded: chain R residue 172 PHE Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 314 GLN Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 43 LYS Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 88 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 106 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 37 optimal weight: 0.0370 chunk 109 optimal weight: 1.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 HIS ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.130491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.104363 restraints weight = 11863.606| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.47 r_work: 0.3263 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9035 Z= 0.125 Angle : 0.564 12.114 12258 Z= 0.287 Chirality : 0.041 0.133 1401 Planarity : 0.004 0.058 1534 Dihedral : 3.815 19.967 1284 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.79 % Allowed : 17.09 % Favored : 81.12 % 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: 1.21 (0.26), residues: 1119 helix: 2.82 (0.27), residues: 387 sheet: 0.54 (0.30), residues: 305 loop : -0.94 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 134 TYR 0.013 0.001 TYR S 190 PHE 0.030 0.001 PHE R 36 TRP 0.008 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 9032) covalent geometry : angle 0.56334 / 0.29 (12252) SS BOND : bond 0.00552 / 0.27 ( 3) SS BOND : angle 1.28248 / 0.72 ( 6) hydrogen bonds : bond 0.04639 / 3.19 ( 418) hydrogen bonds : angle 3.91053 / 2.70 ( 1203) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3680.27 seconds wall clock time: 63 minutes 22.57 seconds (3802.57 seconds total)