Starting phenix.real_space_refine on Fri Jun 5 08:30:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p0k_71079/06_2026/9p0k_71079.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p0k_71079/06_2026/9p0k_71079.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9p0k_71079/06_2026/9p0k_71079.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p0k_71079/06_2026/9p0k_71079.map" model { file = "/net/cci-nas-00/data/ceres_data/9p0k_71079/06_2026/9p0k_71079.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p0k_71079/06_2026/9p0k_71079.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.030 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: 5 Type Number sf(0) Gaussians S 67 5.16 5 C 5984 2.51 5 N 1629 2.21 5 O 1750 1.98 5 H 9401 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 18831 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 4732 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain: "B" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1134 Classifications: {'peptide': 72} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 67} Chain: "C" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3498 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "D" Number of atoms: 5092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 5092 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "E" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 861 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "F" Number of atoms: 3514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3514 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Time building chain proxies: 3.56, per 1000 atoms: 0.19 Number of scatterers: 18831 At special positions: 0 Unit cell: (95.03, 118.422, 149.124, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 67 16.00 O 1750 8.00 N 1629 7.00 C 5984 6.00 H 9401 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 290 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 203 " distance=2.03 Simple disulfide: pdb=" SG CYS B 9 " - pdb=" SG CYS B 36 " distance=2.03 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS B 52 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 99 " distance=2.03 Simple disulfide: pdb=" SG CYS F 160 " - pdb=" SG CYS F 230 " 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: 1.21 Conformation dependent library (CDL) restraints added in 619.4 milliseconds 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2260 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 16 sheets defined 40.5% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 45 through 81 removed outlier: 3.882A pdb=" N PHE A 51 " --> pdb=" O PHE A 47 " (cutoff:3.500A) Proline residue: A 57 - end of helix removed outlier: 4.469A pdb=" N ARG A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 115 removed outlier: 3.598A pdb=" N LEU A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Proline residue: A 107 - end of helix Processing helix chain 'A' and resid 119 through 154 removed outlier: 3.807A pdb=" N LEU A 123 " --> pdb=" O PHE A 119 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR A 136 " --> pdb=" O ASN A 132 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY A 138 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 163 Processing helix chain 'A' and resid 166 through 189 Proline residue: A 185 - end of helix Processing helix chain 'A' and resid 208 through 224 Processing helix chain 'A' and resid 224 through 245 removed outlier: 3.743A pdb=" N TYR A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 283 removed outlier: 4.297A pdb=" N ARG A 252 " --> pdb=" O GLN A 248 " (cutoff:3.500A) Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 289 through 319 removed outlier: 4.211A pdb=" N ARG A 295 " --> pdb=" O GLY A 291 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Proline residue: A 315 - end of helix Processing helix chain 'A' and resid 322 through 335 Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 57 through 72 removed outlier: 3.566A pdb=" N SER B 72 " --> pdb=" O GLU B 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 32 Processing helix chain 'C' and resid 45 through 54 removed outlier: 3.573A pdb=" N ILE C 49 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 removed outlier: 4.365A pdb=" N TRP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 216 Processing helix chain 'C' and resid 227 through 231 removed outlier: 4.228A pdb=" N ASP C 231 " --> pdb=" O SER C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 256 through 260 removed outlier: 3.885A pdb=" N THR C 260 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 removed outlier: 4.035A pdb=" N GLU C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.539A pdb=" N ILE C 285 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 310 removed outlier: 3.934A pdb=" N LEU C 310 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 327 No H-bonds generated for 'chain 'C' and resid 325 through 327' Processing helix chain 'C' and resid 329 through 351 Processing helix chain 'D' and resid 5 through 26 Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'E' and resid 9 through 25 removed outlier: 4.188A pdb=" N ILE E 25 " --> pdb=" O MET E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 46 removed outlier: 4.374A pdb=" N LYS E 46 " --> pdb=" O GLU E 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 35 Processing helix chain 'F' and resid 56 through 59 Processing helix chain 'F' and resid 77 through 79 No H-bonds generated for 'chain 'F' and resid 77 through 79' Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 221 through 225 Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 193 removed outlier: 3.628A pdb=" N HIS A 193 " --> pdb=" O HIS A 202 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS A 202 " --> pdb=" O HIS A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 24 through 30 removed outlier: 4.193A pdb=" N ASP B 26 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU B 40 " --> pdb=" O PHE B 30 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 185 through 187 removed outlier: 6.275A pdb=" N VAL C 34 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N PHE C 199 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU C 36 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU C 39 " --> pdb=" O CYS C 224 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE C 264 " --> pdb=" O TYR C 320 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N HIS C 322 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU C 266 " --> pdb=" O HIS C 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 47 through 51 removed outlier: 3.714A pdb=" N LEU D 336 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 58 through 63 removed outlier: 3.849A pdb=" N ALA D 60 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER D 74 " --> pdb=" O LYS D 78 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS D 91 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASP D 83 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LYS D 89 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 100 through 105 removed outlier: 6.772A pdb=" N GLY D 115 " --> pdb=" O MET D 101 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N CYS D 103 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA D 113 " --> pdb=" O CYS D 103 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N TYR D 105 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N TYR D 111 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N CYS D 121 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLU D 138 " --> pdb=" O CYS D 121 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE D 123 " --> pdb=" O SER D 136 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 146 through 151 removed outlier: 6.363A pdb=" N ASP D 170 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLN D 176 " --> pdb=" O ASP D 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 187 through 192 removed outlier: 6.789A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA D 208 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N THR D 221 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU D 210 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP D 212 " --> pdb=" O MET D 217 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET D 217 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 229 through 234 removed outlier: 6.658A pdb=" N CYS D 250 " --> pdb=" O THR D 263 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N THR D 263 " --> pdb=" O CYS D 250 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU D 252 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN D 259 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 277 through 278 removed outlier: 6.127A pdb=" N ASP D 298 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG D 304 " --> pdb=" O ASP D 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 6 through 10 removed outlier: 3.577A pdb=" N SER F 28 " --> pdb=" O GLN F 6 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU F 23 " --> pdb=" O LEU F 84 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 14 through 15 removed outlier: 5.831A pdb=" N ARG F 41 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N TRP F 50 " --> pdb=" O ARG F 41 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 14 through 15 removed outlier: 4.452A pdb=" N PHE F 113 " --> pdb=" O ARG F 101 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 141 through 143 Processing sheet with id=AB6, first strand: chain 'F' and resid 195 through 196 removed outlier: 3.835A pdb=" N ARG F 192 " --> pdb=" O ASN F 195 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TRP F 177 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N TYR F 191 " --> pdb=" O LEU F 175 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LEU F 175 " --> pdb=" O TYR F 191 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL F 227 " --> pdb=" O GLN F 180 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR F 239 " --> pdb=" O GLN F 232 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 195 through 196 removed outlier: 3.835A pdb=" N ARG F 192 " --> pdb=" O ASN F 195 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TRP F 177 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N TYR F 191 " --> pdb=" O LEU F 175 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LEU F 175 " --> pdb=" O TYR F 191 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL F 227 " --> pdb=" O GLN F 180 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR F 244 " --> pdb=" O TYR F 228 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1344 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: 4.02 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9372 1.03 - 1.23: 126 1.23 - 1.43: 3943 1.43 - 1.62: 5486 1.62 - 1.82: 93 Bond restraints: 19020 Sorted by residual: bond pdb=" N THR B 1 " pdb=" H3 THR B 1 " ideal model delta sigma weight residual 0.890 0.959 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" N THR B 1 " pdb=" H2 THR B 1 " ideal model delta sigma weight residual 0.890 0.958 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" N ASP F 138 " pdb=" CA ASP F 138 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.15e+00 bond pdb=" N THR C 4 " pdb=" CA THR C 4 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N ASP F 4 " pdb=" CA ASP F 4 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 ... (remaining 19015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 32589 1.23 - 2.47: 1548 2.47 - 3.70: 102 3.70 - 4.93: 44 4.93 - 6.17: 6 Bond angle restraints: 34289 Sorted by residual: angle pdb=" C LYS C 192 " pdb=" CA LYS C 192 " pdb=" CB LYS C 192 " ideal model delta sigma weight residual 115.79 111.53 4.26 1.19e+00 7.06e-01 1.28e+01 angle pdb=" C PHE A 187 " pdb=" N ILE A 188 " pdb=" CA ILE A 188 " ideal model delta sigma weight residual 122.35 118.56 3.79 1.18e+00 7.18e-01 1.03e+01 angle pdb=" C ILE A 133 " pdb=" CA ILE A 133 " pdb=" CB ILE A 133 " ideal model delta sigma weight residual 112.24 108.48 3.76 1.34e+00 5.57e-01 7.89e+00 angle pdb=" CA LYS B 66 " pdb=" CB LYS B 66 " pdb=" CG LYS B 66 " ideal model delta sigma weight residual 114.10 118.48 -4.38 2.00e+00 2.50e-01 4.80e+00 angle pdb=" H1 THR B 1 " pdb=" N THR B 1 " pdb=" H3 THR B 1 " ideal model delta sigma weight residual 109.47 103.30 6.17 3.00e+00 1.11e-01 4.22e+00 ... (remaining 34284 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 8102 17.95 - 35.90: 649 35.90 - 53.85: 166 53.85 - 71.81: 43 71.81 - 89.76: 4 Dihedral angle restraints: 8964 sinusoidal: 4829 harmonic: 4135 Sorted by residual: dihedral pdb=" CA ARG F 192 " pdb=" C ARG F 192 " pdb=" N MET F 193 " pdb=" CA MET F 193 " ideal model delta harmonic sigma weight residual -180.00 -158.25 -21.75 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA PHE D 234 " pdb=" C PHE D 234 " pdb=" N PHE D 235 " pdb=" CA PHE D 235 " ideal model delta harmonic sigma weight residual 180.00 159.91 20.09 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA THR D 249 " pdb=" C THR D 249 " pdb=" N CYS D 250 " pdb=" CA CYS D 250 " ideal model delta harmonic sigma weight residual 180.00 160.74 19.26 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 8961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 838 0.027 - 0.054: 423 0.054 - 0.081: 131 0.081 - 0.107: 54 0.107 - 0.134: 42 Chirality restraints: 1488 Sorted by residual: chirality pdb=" CA ILE B 42 " pdb=" N ILE B 42 " pdb=" C ILE B 42 " pdb=" CB ILE B 42 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA ILE C 265 " pdb=" N ILE C 265 " pdb=" C ILE C 265 " pdb=" CB ILE C 265 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CA ILE D 81 " pdb=" N ILE D 81 " pdb=" C ILE D 81 " pdb=" CB ILE D 81 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 1485 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 221 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.68e+00 pdb=" C VAL A 221 " 0.037 2.00e-02 2.50e+03 pdb=" O VAL A 221 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA A 222 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 226 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO A 227 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 227 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 227 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 64 " -0.014 2.00e-02 2.50e+03 9.00e-03 2.43e+00 pdb=" CG PHE A 64 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 64 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 64 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 64 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 64 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 64 " -0.005 2.00e-02 2.50e+03 pdb=" HD1 PHE A 64 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE A 64 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 64 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE A 64 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE A 64 " 0.000 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1356 2.21 - 2.81: 40216 2.81 - 3.41: 51636 3.41 - 4.00: 68509 4.00 - 4.60: 105157 Nonbonded interactions: 266874 Sorted by model distance: nonbonded pdb=" OD2 ASP A 282 " pdb=" HZ2 LYS B 6 " model vdw 1.614 2.450 nonbonded pdb=" H PHE D 235 " pdb=" O ALA D 240 " model vdw 1.635 2.450 nonbonded pdb="HH21 ARG A 197 " pdb=" OG SER B 10 " model vdw 1.644 2.450 nonbonded pdb=" O ILE D 58 " pdb=" HG SER D 316 " model vdw 1.647 2.450 nonbonded pdb=" O VAL C 225 " pdb=" H ASN C 269 " model vdw 1.664 2.450 ... (remaining 266869 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 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: 0.120 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.710 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9625 Z= 0.165 Angle : 0.588 6.146 13040 Z= 0.311 Chirality : 0.040 0.134 1488 Planarity : 0.004 0.049 1653 Dihedral : 13.603 89.758 3468 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.25), residues: 1193 helix: 1.01 (0.25), residues: 422 sheet: -0.85 (0.31), residues: 292 loop : 0.01 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 81 TYR 0.016 0.002 TYR A 308 PHE 0.026 0.002 PHE A 64 TRP 0.008 0.001 TRP B 67 HIS 0.009 0.001 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 9619) covalent geometry : angle 0.58677 / 0.31 (13028) SS BOND : bond 0.00214 / 0.15 ( 6) SS BOND : angle 1.40938 / 0.84 ( 12) hydrogen bonds : bond 0.17151 / 11.48 ( 462) hydrogen bonds : angle 7.33954 / 5.23 ( 1344) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 205 ARG cc_start: 0.8117 (mpt90) cc_final: 0.7859 (mpt90) REVERT: C 243 MET cc_start: 0.6461 (tmm) cc_final: 0.6145 (tmm) REVERT: C 349 LYS cc_start: 0.8702 (ttmt) cc_final: 0.8475 (ttpp) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.3120 time to fit residues: 70.9589 Evaluate side-chains 153 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.1980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 HIS D 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.133638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.103842 restraints weight = 42394.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.107416 restraints weight = 34511.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.108891 restraints weight = 22822.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.109913 restraints weight = 14313.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.111888 restraints weight = 12970.549| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9625 Z= 0.179 Angle : 0.559 5.709 13040 Z= 0.304 Chirality : 0.040 0.157 1488 Planarity : 0.004 0.056 1653 Dihedral : 4.658 34.236 1310 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.97 % Allowed : 5.26 % Favored : 93.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.25), residues: 1193 helix: 1.18 (0.25), residues: 425 sheet: -0.79 (0.30), residues: 291 loop : -0.03 (0.31), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 208 TYR 0.011 0.001 TYR F 191 PHE 0.014 0.001 PHE A 64 TRP 0.007 0.001 TRP D 339 HIS 0.005 0.001 HIS A 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 ( 9619) covalent geometry : angle 0.55810 / 0.30 (13028) SS BOND : bond 0.00420 / 0.29 ( 6) SS BOND : angle 1.21970 / 0.81 ( 12) hydrogen bonds : bond 0.05217 / 3.57 ( 462) hydrogen bonds : angle 5.73045 / 4.08 ( 1344) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 159 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6673 (ptp90) REVERT: A 308 TYR cc_start: 0.9109 (m-10) cc_final: 0.8649 (m-10) REVERT: B 27 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6807 (pp) REVERT: C 230 TYR cc_start: 0.5612 (p90) cc_final: 0.5369 (p90) REVERT: C 349 LYS cc_start: 0.8706 (ttmt) cc_final: 0.8472 (ttpp) REVERT: D 262 MET cc_start: 0.7652 (ptm) cc_final: 0.7341 (ptm) REVERT: F 141 MET cc_start: 0.8599 (mmm) cc_final: 0.8045 (mmm) outliers start: 10 outliers final: 4 residues processed: 164 average time/residue: 0.3200 time to fit residues: 67.5781 Evaluate side-chains 159 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 153 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain D residue 243 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 8 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.133444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.103360 restraints weight = 42731.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.106731 restraints weight = 34613.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.108335 restraints weight = 22964.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.109642 restraints weight = 14553.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.110621 restraints weight = 13286.131| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9625 Z= 0.163 Angle : 0.534 6.705 13040 Z= 0.288 Chirality : 0.040 0.166 1488 Planarity : 0.004 0.058 1653 Dihedral : 4.542 31.265 1310 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.97 % Allowed : 6.52 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.25), residues: 1193 helix: 1.50 (0.25), residues: 418 sheet: -0.89 (0.29), residues: 291 loop : 0.05 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 208 TYR 0.010 0.001 TYR F 191 PHE 0.013 0.001 PHE A 64 TRP 0.010 0.001 TRP D 339 HIS 0.005 0.001 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 9619) covalent geometry : angle 0.53263 / 0.29 (13028) SS BOND : bond 0.00798 / 0.39 ( 6) SS BOND : angle 1.16542 / 0.75 ( 12) hydrogen bonds : bond 0.04391 / 3.05 ( 462) hydrogen bonds : angle 5.25961 / 3.72 ( 1344) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 230 TYR cc_start: 0.5675 (p90) cc_final: 0.5462 (p90) REVERT: C 349 LYS cc_start: 0.8717 (ttmt) cc_final: 0.8496 (ttpp) REVERT: D 65 THR cc_start: 0.8507 (m) cc_final: 0.8259 (p) REVERT: D 262 MET cc_start: 0.7654 (ptm) cc_final: 0.7347 (ptm) REVERT: E 18 GLN cc_start: 0.7451 (tt0) cc_final: 0.6608 (tp-100) REVERT: F 141 MET cc_start: 0.8793 (mmm) cc_final: 0.8374 (mmm) outliers start: 10 outliers final: 6 residues processed: 166 average time/residue: 0.3260 time to fit residues: 69.7892 Evaluate side-chains 161 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 155 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 21 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 88 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 65 optimal weight: 0.0030 chunk 83 optimal weight: 0.1980 chunk 93 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN D 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.134466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.105064 restraints weight = 42366.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.107979 restraints weight = 33916.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.109932 restraints weight = 22164.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.110783 restraints weight = 14266.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.112628 restraints weight = 13049.972| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9625 Z= 0.118 Angle : 0.508 6.241 13040 Z= 0.271 Chirality : 0.039 0.157 1488 Planarity : 0.003 0.038 1653 Dihedral : 4.363 27.056 1310 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.49 % Allowed : 8.28 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.25), residues: 1193 helix: 1.78 (0.25), residues: 418 sheet: -0.77 (0.31), residues: 272 loop : 0.03 (0.30), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 208 TYR 0.010 0.001 TYR F 191 PHE 0.014 0.001 PHE A 64 TRP 0.010 0.001 TRP D 339 HIS 0.004 0.001 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 9619) covalent geometry : angle 0.50744 / 0.27 (13028) SS BOND : bond 0.00445 / 0.27 ( 6) SS BOND : angle 0.99441 / 0.65 ( 12) hydrogen bonds : bond 0.03944 / 2.75 ( 462) hydrogen bonds : angle 4.97500 / 3.53 ( 1344) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 159 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.8180 (m-30) cc_final: 0.7529 (m-30) REVERT: A 292 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.6423 (ptp90) REVERT: C 201 VAL cc_start: 0.9020 (m) cc_final: 0.8719 (p) REVERT: C 243 MET cc_start: 0.6923 (tmm) cc_final: 0.6674 (tmm) REVERT: C 349 LYS cc_start: 0.8744 (ttmt) cc_final: 0.8501 (ttpp) REVERT: D 65 THR cc_start: 0.8429 (m) cc_final: 0.8214 (p) REVERT: D 262 MET cc_start: 0.7602 (ptm) cc_final: 0.7371 (ptm) REVERT: E 18 GLN cc_start: 0.7631 (tt0) cc_final: 0.6373 (tp40) REVERT: E 32 LYS cc_start: 0.7961 (tptp) cc_final: 0.7676 (tppt) REVERT: F 141 MET cc_start: 0.8835 (mmm) cc_final: 0.8502 (mmm) outliers start: 5 outliers final: 4 residues processed: 162 average time/residue: 0.3226 time to fit residues: 67.5106 Evaluate side-chains 161 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 156 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain D residue 243 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 20 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 GLN D 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.133467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.103534 restraints weight = 42425.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.106617 restraints weight = 34610.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.108551 restraints weight = 22759.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.109374 restraints weight = 14720.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.111402 restraints weight = 13360.976| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9625 Z= 0.156 Angle : 0.508 5.278 13040 Z= 0.273 Chirality : 0.039 0.154 1488 Planarity : 0.003 0.058 1653 Dihedral : 4.413 36.137 1310 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.88 % Allowed : 9.54 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.25), residues: 1193 helix: 1.84 (0.25), residues: 418 sheet: -0.87 (0.30), residues: 274 loop : 0.01 (0.30), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 208 TYR 0.010 0.001 TYR F 191 PHE 0.013 0.001 PHE A 64 TRP 0.007 0.001 TRP D 339 HIS 0.004 0.001 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 ( 9619) covalent geometry : angle 0.50754 / 0.27 (13028) SS BOND : bond 0.00323 / 0.23 ( 6) SS BOND : angle 1.02556 / 0.67 ( 12) hydrogen bonds : bond 0.03952 / 2.77 ( 462) hydrogen bonds : angle 4.91009 / 3.49 ( 1344) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 160 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 GLN cc_start: 0.7214 (tp40) cc_final: 0.6366 (mp10) REVERT: C 201 VAL cc_start: 0.9014 (m) cc_final: 0.8704 (p) REVERT: C 243 MET cc_start: 0.6810 (tmm) cc_final: 0.6452 (tmm) REVERT: C 349 LYS cc_start: 0.8744 (ttmt) cc_final: 0.8494 (ttpp) REVERT: D 65 THR cc_start: 0.8456 (m) cc_final: 0.8249 (p) REVERT: D 262 MET cc_start: 0.7653 (ptm) cc_final: 0.7423 (ptm) REVERT: D 325 MET cc_start: 0.8494 (mmm) cc_final: 0.8159 (mmm) REVERT: E 32 LYS cc_start: 0.7911 (tptp) cc_final: 0.7608 (tppt) REVERT: F 45 GLU cc_start: 0.7706 (tp30) cc_final: 0.7458 (tp30) REVERT: F 141 MET cc_start: 0.8926 (mmm) cc_final: 0.8655 (mmm) REVERT: F 219 ARG cc_start: 0.7916 (mpp80) cc_final: 0.7201 (mpp80) outliers start: 9 outliers final: 6 residues processed: 166 average time/residue: 0.3203 time to fit residues: 68.4400 Evaluate side-chains 159 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 153 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 243 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 85 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 44 optimal weight: 0.3980 chunk 60 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.134260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.096743 restraints weight = 42248.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.101165 restraints weight = 20430.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.103827 restraints weight = 13770.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.105262 restraints weight = 11093.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.105889 restraints weight = 9888.089| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9625 Z= 0.121 Angle : 0.498 5.029 13040 Z= 0.266 Chirality : 0.039 0.160 1488 Planarity : 0.003 0.058 1653 Dihedral : 4.315 35.485 1310 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.68 % Allowed : 10.52 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.25), residues: 1193 helix: 2.01 (0.25), residues: 418 sheet: -0.84 (0.30), residues: 275 loop : 0.03 (0.30), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 208 TYR 0.009 0.001 TYR F 191 PHE 0.014 0.001 PHE A 64 TRP 0.009 0.001 TRP D 339 HIS 0.004 0.001 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 9619) covalent geometry : angle 0.49744 / 0.27 (13028) SS BOND : bond 0.00349 / 0.24 ( 6) SS BOND : angle 0.98239 / 0.64 ( 12) hydrogen bonds : bond 0.03734 / 2.62 ( 462) hydrogen bonds : angle 4.73567 / 3.36 ( 1344) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 156 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 GLN cc_start: 0.7178 (tp40) cc_final: 0.6333 (mp10) REVERT: C 201 VAL cc_start: 0.8985 (m) cc_final: 0.8682 (p) REVERT: D 65 THR cc_start: 0.8412 (m) cc_final: 0.8209 (p) REVERT: D 325 MET cc_start: 0.8471 (mmm) cc_final: 0.8108 (mmm) REVERT: E 32 LYS cc_start: 0.7959 (tptp) cc_final: 0.7725 (tppt) REVERT: F 45 GLU cc_start: 0.7640 (tp30) cc_final: 0.7317 (tp30) outliers start: 7 outliers final: 5 residues processed: 161 average time/residue: 0.3309 time to fit residues: 68.4946 Evaluate side-chains 160 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 155 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain D residue 243 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 90 optimal weight: 0.5980 chunk 92 optimal weight: 0.4980 chunk 58 optimal weight: 3.9990 chunk 34 optimal weight: 0.0970 chunk 106 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 96 optimal weight: 0.4980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN D 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.134398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.104780 restraints weight = 42495.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.107467 restraints weight = 34709.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.109729 restraints weight = 22542.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.110316 restraints weight = 14591.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.112731 restraints weight = 13318.152| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9625 Z= 0.120 Angle : 0.499 5.713 13040 Z= 0.265 Chirality : 0.039 0.150 1488 Planarity : 0.003 0.060 1653 Dihedral : 4.255 34.389 1310 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.88 % Allowed : 10.81 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.25), residues: 1193 helix: 2.12 (0.25), residues: 418 sheet: -0.76 (0.31), residues: 269 loop : -0.02 (0.30), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 208 TYR 0.009 0.001 TYR F 191 PHE 0.013 0.001 PHE A 64 TRP 0.008 0.001 TRP D 339 HIS 0.004 0.001 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 9619) covalent geometry : angle 0.49801 / 0.26 (13028) SS BOND : bond 0.00344 / 0.23 ( 6) SS BOND : angle 0.92780 / 0.60 ( 12) hydrogen bonds : bond 0.03641 / 2.55 ( 462) hydrogen bonds : angle 4.65458 / 3.31 ( 1344) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 GLN cc_start: 0.7229 (tp40) cc_final: 0.6404 (mp10) REVERT: C 201 VAL cc_start: 0.8980 (m) cc_final: 0.8672 (p) REVERT: C 243 MET cc_start: 0.6895 (tmm) cc_final: 0.6458 (tmm) REVERT: D 325 MET cc_start: 0.8474 (mmm) cc_final: 0.8108 (mmm) REVERT: E 32 LYS cc_start: 0.8011 (tptp) cc_final: 0.7786 (tppt) REVERT: F 45 GLU cc_start: 0.7662 (tp30) cc_final: 0.7360 (tp30) outliers start: 9 outliers final: 6 residues processed: 166 average time/residue: 0.3199 time to fit residues: 68.1221 Evaluate side-chains 161 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 155 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain D residue 243 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 115 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.133351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.103625 restraints weight = 42445.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.106382 restraints weight = 34592.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.108439 restraints weight = 22982.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.109345 restraints weight = 14723.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.111324 restraints weight = 13380.607| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9625 Z= 0.154 Angle : 0.517 5.704 13040 Z= 0.276 Chirality : 0.039 0.162 1488 Planarity : 0.004 0.064 1653 Dihedral : 4.290 35.189 1310 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.78 % Allowed : 11.20 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.25), residues: 1193 helix: 2.05 (0.25), residues: 419 sheet: -0.81 (0.31), residues: 269 loop : -0.10 (0.30), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 208 TYR 0.009 0.001 TYR F 191 PHE 0.012 0.001 PHE A 64 TRP 0.008 0.001 TRP D 339 HIS 0.005 0.001 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 9619) covalent geometry : angle 0.51655 / 0.28 (13028) SS BOND : bond 0.00367 / 0.24 ( 6) SS BOND : angle 1.10605 / 0.71 ( 12) hydrogen bonds : bond 0.03757 / 2.63 ( 462) hydrogen bonds : angle 4.67993 / 3.33 ( 1344) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 156 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 GLN cc_start: 0.7228 (tp40) cc_final: 0.6408 (mp10) REVERT: C 201 VAL cc_start: 0.8984 (m) cc_final: 0.8674 (p) REVERT: D 325 MET cc_start: 0.8484 (mmm) cc_final: 0.8128 (mmm) REVERT: F 45 GLU cc_start: 0.7739 (tp30) cc_final: 0.7423 (tp30) outliers start: 8 outliers final: 8 residues processed: 162 average time/residue: 0.3228 time to fit residues: 67.2032 Evaluate side-chains 163 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 155 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 243 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 60 optimal weight: 0.0060 chunk 48 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 10 optimal weight: 0.3980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.134153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.104552 restraints weight = 42416.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.107129 restraints weight = 34572.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.109349 restraints weight = 22767.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.110172 restraints weight = 14545.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.112305 restraints weight = 13250.648| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9625 Z= 0.122 Angle : 0.518 6.338 13040 Z= 0.274 Chirality : 0.039 0.162 1488 Planarity : 0.003 0.064 1653 Dihedral : 4.221 33.579 1310 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.88 % Allowed : 11.68 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.25), residues: 1193 helix: 2.15 (0.25), residues: 419 sheet: -0.75 (0.31), residues: 269 loop : -0.06 (0.30), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 208 TYR 0.009 0.001 TYR F 191 PHE 0.013 0.001 PHE A 64 TRP 0.008 0.001 TRP D 339 HIS 0.003 0.001 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 9619) covalent geometry : angle 0.51718 / 0.27 (13028) SS BOND : bond 0.00351 / 0.23 ( 6) SS BOND : angle 0.94664 / 0.60 ( 12) hydrogen bonds : bond 0.03604 / 2.52 ( 462) hydrogen bonds : angle 4.59642 / 3.27 ( 1344) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 GLN cc_start: 0.7217 (tp40) cc_final: 0.6409 (mp10) REVERT: C 201 VAL cc_start: 0.8967 (m) cc_final: 0.8661 (p) REVERT: C 243 MET cc_start: 0.6861 (tmm) cc_final: 0.6495 (tmm) REVERT: D 325 MET cc_start: 0.8481 (mmm) cc_final: 0.8094 (mmm) REVERT: F 45 GLU cc_start: 0.7745 (tp30) cc_final: 0.7415 (tp30) outliers start: 9 outliers final: 9 residues processed: 165 average time/residue: 0.3250 time to fit residues: 68.9739 Evaluate side-chains 165 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 14 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 chunk 30 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 0.0170 chunk 54 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.133992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.104356 restraints weight = 42343.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.106801 restraints weight = 34632.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.109084 restraints weight = 22879.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.109901 restraints weight = 14612.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.111991 restraints weight = 13311.194| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9625 Z= 0.127 Angle : 0.525 6.375 13040 Z= 0.278 Chirality : 0.039 0.168 1488 Planarity : 0.004 0.070 1653 Dihedral : 4.188 32.471 1310 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.97 % Allowed : 11.49 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.25), residues: 1193 helix: 2.20 (0.25), residues: 419 sheet: -0.74 (0.31), residues: 269 loop : -0.08 (0.30), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 208 TYR 0.008 0.001 TYR F 191 PHE 0.012 0.001 PHE A 64 TRP 0.008 0.001 TRP D 339 HIS 0.003 0.001 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 9619) covalent geometry : angle 0.52439 / 0.28 (13028) SS BOND : bond 0.00317 / 0.21 ( 6) SS BOND : angle 0.95448 / 0.61 ( 12) hydrogen bonds : bond 0.03568 / 2.50 ( 462) hydrogen bonds : angle 4.55691 / 3.25 ( 1344) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 159 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 GLN cc_start: 0.7218 (tp40) cc_final: 0.6311 (mp10) REVERT: B 62 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7599 (tm-30) REVERT: C 201 VAL cc_start: 0.8835 (m) cc_final: 0.8600 (p) REVERT: D 325 MET cc_start: 0.8497 (mmm) cc_final: 0.8114 (mmm) REVERT: F 45 GLU cc_start: 0.7756 (tp30) cc_final: 0.7424 (tp30) REVERT: F 247 GLU cc_start: 0.6937 (pm20) cc_final: 0.6327 (pm20) outliers start: 10 outliers final: 10 residues processed: 165 average time/residue: 0.3156 time to fit residues: 66.9680 Evaluate side-chains 167 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 49 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.132686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.095225 restraints weight = 42391.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.099459 restraints weight = 20631.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.101976 restraints weight = 13965.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.103390 restraints weight = 11289.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.103991 restraints weight = 10093.572| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9625 Z= 0.173 Angle : 0.550 7.100 13040 Z= 0.292 Chirality : 0.039 0.156 1488 Planarity : 0.004 0.067 1653 Dihedral : 4.294 34.660 1310 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.97 % Allowed : 11.98 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.25), residues: 1193 helix: 2.05 (0.25), residues: 419 sheet: -0.80 (0.31), residues: 269 loop : -0.14 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 208 TYR 0.011 0.001 TYR A 150 PHE 0.011 0.001 PHE A 64 TRP 0.006 0.001 TRP D 339 HIS 0.006 0.001 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 9619) covalent geometry : angle 0.54903 / 0.29 (13028) SS BOND : bond 0.00331 / 0.22 ( 6) SS BOND : angle 1.11656 / 0.71 ( 12) hydrogen bonds : bond 0.03784 / 2.66 ( 462) hydrogen bonds : angle 4.68482 / 3.34 ( 1344) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3459.18 seconds wall clock time: 59 minutes 51.65 seconds (3591.65 seconds total)