Starting phenix.real_space_refine on Fri Jul 3 02:50:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8efl_28085/07_2026/8efl_28085.cif Found real_map, /net/cci-nas-00/data/ceres_data/8efl_28085/07_2026/8efl_28085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8efl_28085/07_2026/8efl_28085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8efl_28085/07_2026/8efl_28085.map" model { file = "/net/cci-nas-00/data/ceres_data/8efl_28085/07_2026/8efl_28085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8efl_28085/07_2026/8efl_28085.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8efl_28085/07_2026/8efl_28085.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8efl_28085/07_2026/8efl_28085.cif" } resolution = 3.2 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= 0.008 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 98 5.16 5 Cl 6 4.86 5 C 7645 2.51 5 N 1908 2.21 5 O 2093 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11750 Number of models: 1 Model: "" Number of chains: 9 Chain: "R" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Chain: "A" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1816 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2576 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 329} Chain: "C" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 437 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "E" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1788 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "M" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Chain: "F" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 183 Classifications: {'peptide': 23} Modifications used: {'COO': 1} Link IDs: {'TRANS': 22} Chain: "R" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 166 Unusual residues: {'CLR': 5, 'WH9': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "M" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 166 Unusual residues: {'CLR': 5, 'WH9': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 2.45, per 1000 atoms: 0.21 Number of scatterers: 11750 At special positions: 0 Unit cell: (106.029, 116.739, 153.153, 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) Cl 6 17.00 S 98 16.00 O 2093 8.00 N 1908 7.00 C 7645 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 142 " - pdb=" SG CYS R 219 " distance=2.03 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.04 Simple disulfide: pdb=" SG CYS M 142 " - pdb=" SG CYS M 219 " 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: 0.98 Conformation dependent library (CDL) restraints added in 561.5 milliseconds 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2734 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 15 sheets defined 49.7% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'R' and resid 66 through 98 Processing helix chain 'R' and resid 103 through 122 Processing helix chain 'R' and resid 122 through 133 removed outlier: 3.730A pdb=" N GLN R 126 " --> pdb=" O THR R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 173 Processing helix chain 'R' and resid 173 through 181 removed outlier: 3.826A pdb=" N ASP R 179 " --> pdb=" O VAL R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 207 removed outlier: 4.031A pdb=" N ILE R 200 " --> pdb=" O LEU R 196 " (cutoff:3.500A) Proline residue: R 203 - end of helix Processing helix chain 'R' and resid 226 through 264 removed outlier: 3.640A pdb=" N TRP R 230 " --> pdb=" O PRO R 226 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N MET R 245 " --> pdb=" O PHE R 241 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 270 through 308 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 313 through 339 removed outlier: 3.939A pdb=" N ASN R 330 " --> pdb=" O LEU R 326 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER R 331 " --> pdb=" O GLY R 327 " (cutoff:3.500A) Proline residue: R 335 - end of helix Processing helix chain 'R' and resid 342 through 352 Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.597A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.207A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 217 removed outlier: 4.552A pdb=" N GLY A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.845A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 327 through 352 removed outlier: 3.832A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 11 through 24 Processing helix chain 'C' and resid 29 through 45 removed outlier: 3.569A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.306A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.616A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'M' and resid 67 through 98 Processing helix chain 'M' and resid 103 through 121 Processing helix chain 'M' and resid 122 through 133 removed outlier: 3.535A pdb=" N GLN M 126 " --> pdb=" O THR M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 138 through 173 removed outlier: 3.689A pdb=" N PHE M 154 " --> pdb=" O TYR M 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 181 removed outlier: 3.807A pdb=" N ASP M 179 " --> pdb=" O VAL M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 182 through 207 removed outlier: 3.745A pdb=" N ILE M 200 " --> pdb=" O LEU M 196 " (cutoff:3.500A) Proline residue: M 203 - end of helix Processing helix chain 'M' and resid 226 through 264 removed outlier: 3.587A pdb=" N TRP M 230 " --> pdb=" O PRO M 226 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N MET M 245 " --> pdb=" O PHE M 241 " (cutoff:3.500A) Proline residue: M 246 - end of helix Processing helix chain 'M' and resid 270 through 308 Proline residue: M 297 - end of helix Processing helix chain 'M' and resid 313 through 340 removed outlier: 3.745A pdb=" N SER M 331 " --> pdb=" O GLY M 327 " (cutoff:3.500A) Proline residue: M 335 - end of helix Processing helix chain 'M' and resid 342 through 352 Processing helix chain 'F' and resid 333 through 352 Processing sheet with id=AA1, first strand: chain 'R' and resid 208 through 213 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.806A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.298A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.738A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.734A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.791A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.740A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.398A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.711A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.672A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.672A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 147 through 149 removed outlier: 3.761A pdb=" N GLU E 247 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU E 175 " --> pdb=" O TYR E 191 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N TYR E 191 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TRP E 177 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 156 through 160 Processing sheet with id=AB6, first strand: chain 'M' and resid 208 through 213 703 hydrogen bonds defined for protein. 2040 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: 2.00 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1808 1.30 - 1.43: 3148 1.43 - 1.56: 6917 1.56 - 1.69: 9 1.69 - 1.82: 151 Bond restraints: 12033 Sorted by residual: bond pdb=" C03 WH9 R 401 " pdb=" N01 WH9 R 401 " ideal model delta sigma weight residual 1.380 1.316 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C03 WH9 M 401 " pdb=" N01 WH9 M 401 " ideal model delta sigma weight residual 1.380 1.316 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C07 WH9 R 401 " pdb=" N02 WH9 R 401 " ideal model delta sigma weight residual 1.391 1.328 0.063 2.00e-02 2.50e+03 9.94e+00 bond pdb=" C07 WH9 M 401 " pdb=" N02 WH9 M 401 " ideal model delta sigma weight residual 1.391 1.329 0.062 2.00e-02 2.50e+03 9.76e+00 bond pdb=" C07 WH9 M 401 " pdb=" N01 WH9 M 401 " ideal model delta sigma weight residual 1.380 1.322 0.058 2.00e-02 2.50e+03 8.32e+00 ... (remaining 12028 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 15520 1.77 - 3.54: 704 3.54 - 5.30: 121 5.30 - 7.07: 26 7.07 - 8.84: 8 Bond angle restraints: 16379 Sorted by residual: angle pdb=" C ARG E 192 " pdb=" N MET E 193 " pdb=" CA MET E 193 " ideal model delta sigma weight residual 121.54 130.25 -8.71 1.91e+00 2.74e-01 2.08e+01 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 124.82 130.69 -5.87 1.78e+00 3.16e-01 1.09e+01 angle pdb=" N LEU R 123 " pdb=" CA LEU R 123 " pdb=" C LEU R 123 " ideal model delta sigma weight residual 109.81 116.89 -7.08 2.21e+00 2.05e-01 1.03e+01 angle pdb=" C GLY E 210 " pdb=" N THR E 211 " pdb=" CA THR E 211 " ideal model delta sigma weight residual 125.66 131.49 -5.83 1.85e+00 2.92e-01 9.92e+00 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 123.47 128.11 -4.64 1.53e+00 4.27e-01 9.18e+00 ... (remaining 16374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.15: 6734 14.15 - 28.29: 266 28.29 - 42.44: 41 42.44 - 56.58: 6 56.58 - 70.73: 2 Dihedral angle restraints: 7049 sinusoidal: 2821 harmonic: 4228 Sorted by residual: dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 158.57 21.43 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 161.40 18.60 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ILE B 81 " pdb=" C ILE B 81 " pdb=" N TRP B 82 " pdb=" CA TRP B 82 " ideal model delta harmonic sigma weight residual -180.00 -164.07 -15.93 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 7046 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1699 0.088 - 0.176: 168 0.176 - 0.264: 25 0.264 - 0.352: 8 0.352 - 0.440: 11 Chirality restraints: 1911 Sorted by residual: chirality pdb=" C14 CLR M 405 " pdb=" C13 CLR M 405 " pdb=" C15 CLR M 405 " pdb=" C8 CLR M 405 " both_signs ideal model delta sigma weight residual False -2.32 -2.76 0.44 2.00e-01 2.50e+01 4.83e+00 chirality pdb=" C14 CLR M 402 " pdb=" C13 CLR M 402 " pdb=" C15 CLR M 402 " pdb=" C8 CLR M 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" C14 CLR R 403 " pdb=" C13 CLR R 403 " pdb=" C15 CLR R 403 " pdb=" C8 CLR R 403 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.29e+00 ... (remaining 1908 not shown) Planarity restraints: 1969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.050 5.00e-02 4.00e+02 7.53e-02 9.07e+00 pdb=" N PRO B 236 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 278 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.86e+00 pdb=" C ARG R 278 " -0.038 2.00e-02 2.50e+03 pdb=" O ARG R 278 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG R 279 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO B 194 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.025 5.00e-02 4.00e+02 ... (remaining 1966 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2204 2.79 - 3.32: 10638 3.32 - 3.84: 19028 3.84 - 4.37: 21433 4.37 - 4.90: 38718 Nonbonded interactions: 92021 Sorted by model distance: nonbonded pdb=" O ALA M 325 " pdb=" OG1 THR M 329 " model vdw 2.259 3.040 nonbonded pdb=" OG SER E 205 " pdb=" OG1 THR E 216 " model vdw 2.279 3.040 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.304 3.040 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.321 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.330 3.040 ... (remaining 92016 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 Found NCS groups: ncs_group { reference = chain 'M' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.700 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 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 : 0.005 0.064 12036 Z= 0.250 Angle : 0.868 8.841 16385 Z= 0.463 Chirality : 0.066 0.440 1911 Planarity : 0.006 0.075 1969 Dihedral : 8.194 70.730 4306 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.35 (0.20), residues: 1428 helix: 1.12 (0.17), residues: 664 sheet: 0.57 (0.30), residues: 283 loop : -1.19 (0.24), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 314 TYR 0.024 0.002 TYR R 108 PHE 0.026 0.002 PHE A 189 TRP 0.027 0.002 TRP E 111 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.25 (12033) covalent geometry : angle 0.86737 / 0.46 (16379) SS BOND : bond 0.00588 / 0.29 ( 3) SS BOND : angle 1.90709 / 1.04 ( 6) hydrogen bonds : bond 0.11270 / 6.83 ( 698) hydrogen bonds : angle 5.75249 / 4.23 ( 2040) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.449 Fit side-chains REVERT: R 260 ARG cc_start: 0.7467 (tpt90) cc_final: 0.7009 (tpp80) REVERT: A 44 SER cc_start: 0.7619 (m) cc_final: 0.7127 (p) REVERT: A 309 ASP cc_start: 0.7249 (m-30) cc_final: 0.7039 (m-30) REVERT: B 150 ARG cc_start: 0.8430 (mmt-90) cc_final: 0.8179 (mpt180) REVERT: B 175 GLN cc_start: 0.7608 (mm110) cc_final: 0.7160 (mm110) REVERT: B 189 SER cc_start: 0.8838 (p) cc_final: 0.8480 (t) REVERT: E 167 LEU cc_start: 0.7827 (tp) cc_final: 0.7541 (tp) REVERT: M 266 MET cc_start: 0.5980 (tmt) cc_final: 0.5721 (ttp) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.1139 time to fit residues: 39.3027 Evaluate side-chains 160 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.0020 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 173 HIS R 190 ASN R 330 ASN B 35 ASN B 91 HIS B 155 ASN B 156 GLN B 266 HIS B 293 ASN E 77 ASN E 180 GLN M 330 ASN M 334 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.188843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.149158 restraints weight = 12395.083| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.28 r_work: 0.3465 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12036 Z= 0.109 Angle : 0.480 6.927 16385 Z= 0.256 Chirality : 0.038 0.150 1911 Planarity : 0.004 0.056 1969 Dihedral : 4.744 66.483 1694 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.90 % Allowed : 7.04 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.58 (0.21), residues: 1428 helix: 2.54 (0.18), residues: 671 sheet: 0.57 (0.29), residues: 279 loop : -0.87 (0.25), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 129 TYR 0.019 0.001 TYR E 191 PHE 0.019 0.001 PHE A 189 TRP 0.019 0.001 TRP B 169 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (12033) covalent geometry : angle 0.47930 / 0.26 (16379) SS BOND : bond 0.00475 / 0.23 ( 3) SS BOND : angle 1.07536 / 0.55 ( 6) hydrogen bonds : bond 0.03952 / 2.57 ( 698) hydrogen bonds : angle 4.44556 / 3.28 ( 2040) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.458 Fit side-chains REVERT: R 283 MET cc_start: 0.7979 (ttm) cc_final: 0.7686 (mtp) REVERT: R 310 ILE cc_start: 0.6513 (OUTLIER) cc_final: 0.5697 (tp) REVERT: A 276 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7485 (mm-30) REVERT: A 309 ASP cc_start: 0.8022 (m-30) cc_final: 0.7628 (m-30) REVERT: A 350 ASP cc_start: 0.8191 (t0) cc_final: 0.7630 (m-30) REVERT: B 101 MET cc_start: 0.9093 (mtp) cc_final: 0.8831 (mtp) REVERT: B 130 GLU cc_start: 0.7870 (tt0) cc_final: 0.7564 (mp0) REVERT: B 161 SER cc_start: 0.9234 (OUTLIER) cc_final: 0.8873 (m) REVERT: B 175 GLN cc_start: 0.7876 (mm110) cc_final: 0.7555 (mm-40) REVERT: B 212 ASP cc_start: 0.7898 (t0) cc_final: 0.7630 (t0) REVERT: B 325 MET cc_start: 0.8115 (tpp) cc_final: 0.7668 (mmt) REVERT: E 83 MET cc_start: 0.7383 (mtm) cc_final: 0.7121 (mtp) outliers start: 24 outliers final: 13 residues processed: 177 average time/residue: 0.0920 time to fit residues: 24.4469 Evaluate side-chains 159 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 95 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 101 optimal weight: 20.0000 chunk 116 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 HIS B 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.204591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.162713 restraints weight = 12394.286| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.01 r_work: 0.3302 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12036 Z= 0.188 Angle : 0.563 8.622 16385 Z= 0.291 Chirality : 0.041 0.155 1911 Planarity : 0.004 0.048 1969 Dihedral : 5.349 62.143 1694 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.01 % Allowed : 7.99 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.74 (0.21), residues: 1428 helix: 2.78 (0.19), residues: 661 sheet: 0.48 (0.29), residues: 278 loop : -0.76 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 197 TYR 0.018 0.002 TYR R 301 PHE 0.021 0.002 PHE R 154 TRP 0.021 0.002 TRP B 82 HIS 0.006 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 (12033) covalent geometry : angle 0.56245 / 0.29 (16379) SS BOND : bond 0.00614 / 0.30 ( 3) SS BOND : angle 1.42389 / 0.73 ( 6) hydrogen bonds : bond 0.05094 / 3.38 ( 698) hydrogen bonds : angle 4.49190 / 3.34 ( 2040) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 0.492 Fit side-chains REVERT: R 283 MET cc_start: 0.8315 (ttm) cc_final: 0.8103 (mtp) REVERT: R 310 ILE cc_start: 0.7145 (OUTLIER) cc_final: 0.6089 (tp) REVERT: A 44 SER cc_start: 0.7906 (m) cc_final: 0.7163 (p) REVERT: A 240 MET cc_start: 0.3928 (OUTLIER) cc_final: 0.3320 (mtm) REVERT: A 309 ASP cc_start: 0.8015 (m-30) cc_final: 0.7710 (m-30) REVERT: A 350 ASP cc_start: 0.8625 (t0) cc_final: 0.7974 (m-30) REVERT: B 175 GLN cc_start: 0.8043 (mm110) cc_final: 0.7639 (mm110) REVERT: B 262 MET cc_start: 0.7435 (ttm) cc_final: 0.7079 (ttm) REVERT: E 141 MET cc_start: 0.8452 (mmm) cc_final: 0.7834 (tpp) REVERT: E 232 GLN cc_start: 0.7944 (pp30) cc_final: 0.7673 (pp30) REVERT: M 283 MET cc_start: 0.8204 (tpp) cc_final: 0.7886 (tpp) outliers start: 38 outliers final: 28 residues processed: 184 average time/residue: 0.1062 time to fit residues: 28.9144 Evaluate side-chains 163 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 293 VAL Chi-restraints excluded: chain M residue 332 CYS Chi-restraints excluded: chain F residue 349 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 10 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 123 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 101 optimal weight: 40.0000 chunk 133 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 111 ASN M 334 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.201423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.173591 restraints weight = 12266.174| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 1.23 r_work: 0.3530 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12036 Z= 0.109 Angle : 0.467 6.344 16385 Z= 0.245 Chirality : 0.038 0.168 1911 Planarity : 0.003 0.042 1969 Dihedral : 4.963 59.357 1694 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.14 % Allowed : 9.89 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.95 (0.21), residues: 1428 helix: 2.95 (0.18), residues: 667 sheet: 0.55 (0.30), residues: 271 loop : -0.68 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.014 0.001 TYR R 130 PHE 0.015 0.001 PHE R 154 TRP 0.022 0.001 TRP B 82 HIS 0.002 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (12033) covalent geometry : angle 0.46701 / 0.24 (16379) SS BOND : bond 0.00422 / 0.20 ( 3) SS BOND : angle 1.02970 / 0.53 ( 6) hydrogen bonds : bond 0.03960 / 2.63 ( 698) hydrogen bonds : angle 4.19178 / 3.12 ( 2040) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.460 Fit side-chains REVERT: R 310 ILE cc_start: 0.7078 (OUTLIER) cc_final: 0.6381 (tp) REVERT: A 209 LYS cc_start: 0.8634 (pttt) cc_final: 0.8034 (mtpt) REVERT: A 240 MET cc_start: 0.4047 (OUTLIER) cc_final: 0.3750 (mtm) REVERT: A 309 ASP cc_start: 0.7733 (m-30) cc_final: 0.7442 (m-30) REVERT: A 350 ASP cc_start: 0.8152 (t0) cc_final: 0.7753 (m-30) REVERT: B 175 GLN cc_start: 0.7841 (mm110) cc_final: 0.7484 (mm-40) REVERT: B 262 MET cc_start: 0.7353 (ttm) cc_final: 0.7050 (ttm) REVERT: B 269 ILE cc_start: 0.7808 (mt) cc_final: 0.7559 (pt) REVERT: M 283 MET cc_start: 0.7839 (tpp) cc_final: 0.7519 (tpp) outliers start: 27 outliers final: 19 residues processed: 156 average time/residue: 0.1036 time to fit residues: 24.0917 Evaluate side-chains 157 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain M residue 332 CYS Chi-restraints excluded: chain F residue 349 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 0.4980 chunk 93 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 81 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 6 optimal weight: 0.0980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.205064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.164062 restraints weight = 12202.862| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.31 r_work: 0.3179 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12036 Z= 0.100 Angle : 0.449 5.886 16385 Z= 0.235 Chirality : 0.038 0.139 1911 Planarity : 0.003 0.041 1969 Dihedral : 4.762 56.888 1694 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.45 % Allowed : 10.36 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.22), residues: 1428 helix: 3.14 (0.18), residues: 667 sheet: 0.49 (0.29), residues: 276 loop : -0.55 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.013 0.001 TYR R 151 PHE 0.014 0.001 PHE A 189 TRP 0.020 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (12033) covalent geometry : angle 0.44870 / 0.23 (16379) SS BOND : bond 0.00445 / 0.21 ( 3) SS BOND : angle 1.04165 / 0.52 ( 6) hydrogen bonds : bond 0.03678 / 2.46 ( 698) hydrogen bonds : angle 4.07816 / 3.03 ( 2040) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.533 Fit side-chains REVERT: R 310 ILE cc_start: 0.7154 (OUTLIER) cc_final: 0.6284 (tp) REVERT: A 209 LYS cc_start: 0.8771 (pttt) cc_final: 0.7789 (mtpt) REVERT: A 240 MET cc_start: 0.4266 (OUTLIER) cc_final: 0.3674 (mtm) REVERT: A 309 ASP cc_start: 0.7721 (m-30) cc_final: 0.7419 (m-30) REVERT: A 350 ASP cc_start: 0.8308 (t0) cc_final: 0.7761 (m-30) REVERT: B 175 GLN cc_start: 0.7778 (mm110) cc_final: 0.7470 (mp10) REVERT: B 228 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8272 (p0) REVERT: B 234 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.8637 (m-80) REVERT: B 269 ILE cc_start: 0.6774 (mt) cc_final: 0.6547 (tp) REVERT: E 189 LEU cc_start: 0.8629 (mt) cc_final: 0.8406 (mt) REVERT: M 257 MET cc_start: 0.8866 (ttt) cc_final: 0.8655 (ttp) REVERT: M 283 MET cc_start: 0.7920 (tpp) cc_final: 0.7544 (tpp) outliers start: 31 outliers final: 24 residues processed: 160 average time/residue: 0.1080 time to fit residues: 25.5700 Evaluate side-chains 164 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 332 CYS Chi-restraints excluded: chain F residue 349 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 7 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.197746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.156337 restraints weight = 12202.730| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.24 r_work: 0.3121 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12036 Z= 0.142 Angle : 0.493 6.532 16385 Z= 0.255 Chirality : 0.039 0.146 1911 Planarity : 0.003 0.041 1969 Dihedral : 4.981 56.029 1694 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.69 % Allowed : 10.68 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.22), residues: 1428 helix: 3.03 (0.19), residues: 665 sheet: 0.32 (0.29), residues: 290 loop : -0.46 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 265 TYR 0.015 0.001 TYR E 94 PHE 0.017 0.001 PHE R 154 TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (12033) covalent geometry : angle 0.49264 / 0.25 (16379) SS BOND : bond 0.00440 / 0.21 ( 3) SS BOND : angle 1.07890 / 0.56 ( 6) hydrogen bonds : bond 0.04290 / 2.88 ( 698) hydrogen bonds : angle 4.23441 / 3.14 ( 2040) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 0.469 Fit side-chains REVERT: R 310 ILE cc_start: 0.7360 (OUTLIER) cc_final: 0.6467 (tp) REVERT: A 44 SER cc_start: 0.7743 (m) cc_final: 0.7132 (p) REVERT: A 240 MET cc_start: 0.4398 (OUTLIER) cc_final: 0.3758 (mtm) REVERT: A 309 ASP cc_start: 0.7656 (m-30) cc_final: 0.7402 (m-30) REVERT: A 350 ASP cc_start: 0.8229 (t0) cc_final: 0.7643 (m-30) REVERT: B 175 GLN cc_start: 0.7779 (mm110) cc_final: 0.7436 (mp10) REVERT: B 262 MET cc_start: 0.7495 (ttm) cc_final: 0.7246 (ttm) REVERT: M 283 MET cc_start: 0.7900 (tpp) cc_final: 0.7539 (tpp) outliers start: 34 outliers final: 30 residues processed: 163 average time/residue: 0.1076 time to fit residues: 26.0523 Evaluate side-chains 167 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 293 VAL Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 91 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 116 optimal weight: 0.3980 chunk 85 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.200655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.175128 restraints weight = 12101.445| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 1.14 r_work: 0.3544 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12036 Z= 0.124 Angle : 0.479 6.142 16385 Z= 0.249 Chirality : 0.038 0.145 1911 Planarity : 0.003 0.040 1969 Dihedral : 4.962 53.333 1694 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.77 % Allowed : 10.60 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.22), residues: 1428 helix: 3.08 (0.18), residues: 665 sheet: 0.20 (0.29), residues: 292 loop : -0.45 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 98 TYR 0.015 0.001 TYR E 94 PHE 0.016 0.001 PHE R 154 TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (12033) covalent geometry : angle 0.47901 / 0.25 (16379) SS BOND : bond 0.00455 / 0.22 ( 3) SS BOND : angle 1.10995 / 0.57 ( 6) hydrogen bonds : bond 0.04035 / 2.72 ( 698) hydrogen bonds : angle 4.19242 / 3.11 ( 2040) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.516 Fit side-chains REVERT: R 310 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.6863 (tp) REVERT: A 44 SER cc_start: 0.8045 (m) cc_final: 0.7302 (p) REVERT: A 240 MET cc_start: 0.4957 (OUTLIER) cc_final: 0.4330 (mtm) REVERT: A 309 ASP cc_start: 0.7886 (m-30) cc_final: 0.7659 (m-30) REVERT: A 350 ASP cc_start: 0.8498 (t0) cc_final: 0.8006 (m-30) REVERT: B 175 GLN cc_start: 0.7960 (mm110) cc_final: 0.7703 (mp10) REVERT: B 269 ILE cc_start: 0.7668 (mt) cc_final: 0.7409 (tp) REVERT: E 141 MET cc_start: 0.8251 (mmm) cc_final: 0.7043 (mmm) REVERT: M 283 MET cc_start: 0.8174 (tpp) cc_final: 0.7851 (tpp) outliers start: 35 outliers final: 30 residues processed: 158 average time/residue: 0.1036 time to fit residues: 24.1283 Evaluate side-chains 160 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 148 ILE Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 293 VAL Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 36 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 331 ASN E 180 GLN M 173 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.200690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.158119 restraints weight = 12267.053| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.90 r_work: 0.3098 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12036 Z= 0.165 Angle : 0.527 7.303 16385 Z= 0.272 Chirality : 0.040 0.147 1911 Planarity : 0.004 0.041 1969 Dihedral : 5.223 50.644 1694 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.16 % Allowed : 10.36 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.87 (0.22), residues: 1428 helix: 2.95 (0.19), residues: 662 sheet: 0.24 (0.29), residues: 284 loop : -0.61 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 98 TYR 0.019 0.001 TYR E 94 PHE 0.018 0.001 PHE R 154 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.16 (12033) covalent geometry : angle 0.52623 / 0.27 (16379) SS BOND : bond 0.00484 / 0.23 ( 3) SS BOND : angle 1.11601 / 0.59 ( 6) hydrogen bonds : bond 0.04652 / 3.15 ( 698) hydrogen bonds : angle 4.37161 / 3.24 ( 2040) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.558 Fit side-chains REVERT: R 212 TYR cc_start: 0.7755 (m-80) cc_final: 0.7482 (m-80) REVERT: R 310 ILE cc_start: 0.7572 (OUTLIER) cc_final: 0.6930 (tp) REVERT: A 240 MET cc_start: 0.4952 (OUTLIER) cc_final: 0.4463 (mtm) REVERT: A 309 ASP cc_start: 0.7537 (m-30) cc_final: 0.7332 (m-30) REVERT: A 350 ASP cc_start: 0.8300 (t0) cc_final: 0.7750 (m-30) REVERT: B 101 MET cc_start: 0.9198 (mtm) cc_final: 0.8878 (ptp) REVERT: B 175 GLN cc_start: 0.7868 (mm110) cc_final: 0.7475 (mp10) REVERT: B 262 MET cc_start: 0.7544 (ttm) cc_final: 0.7277 (ttm) REVERT: E 141 MET cc_start: 0.8136 (mmm) cc_final: 0.6914 (mmm) REVERT: E 232 GLN cc_start: 0.7870 (pp30) cc_final: 0.7529 (pp30) REVERT: M 218 ASP cc_start: 0.7253 (t0) cc_final: 0.6790 (p0) REVERT: M 283 MET cc_start: 0.8011 (tpp) cc_final: 0.7648 (tpp) outliers start: 40 outliers final: 34 residues processed: 165 average time/residue: 0.1022 time to fit residues: 25.2766 Evaluate side-chains 166 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 148 ILE Chi-restraints excluded: chain R residue 164 SER Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 293 VAL Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 122 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 7 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 321 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.203468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.164885 restraints weight = 12203.979| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.54 r_work: 0.3379 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12036 Z= 0.117 Angle : 0.486 7.842 16385 Z= 0.252 Chirality : 0.038 0.140 1911 Planarity : 0.003 0.039 1969 Dihedral : 5.021 52.329 1694 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.37 % Allowed : 11.79 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.91 (0.22), residues: 1428 helix: 3.03 (0.19), residues: 664 sheet: 0.14 (0.29), residues: 282 loop : -0.59 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 98 TYR 0.013 0.001 TYR E 94 PHE 0.015 0.001 PHE R 154 TRP 0.022 0.001 TRP B 82 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (12033) covalent geometry : angle 0.48553 / 0.25 (16379) SS BOND : bond 0.00452 / 0.22 ( 3) SS BOND : angle 1.05104 / 0.54 ( 6) hydrogen bonds : bond 0.04004 / 2.70 ( 698) hydrogen bonds : angle 4.27078 / 3.17 ( 2040) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.456 Fit side-chains REVERT: R 212 TYR cc_start: 0.7742 (m-80) cc_final: 0.7443 (m-80) REVERT: R 310 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.6964 (tp) REVERT: A 240 MET cc_start: 0.5102 (OUTLIER) cc_final: 0.4618 (mtm) REVERT: A 309 ASP cc_start: 0.7879 (m-30) cc_final: 0.7677 (m-30) REVERT: A 316 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8279 (p) REVERT: A 350 ASP cc_start: 0.8528 (t0) cc_final: 0.8013 (m-30) REVERT: B 101 MET cc_start: 0.9188 (mtm) cc_final: 0.8841 (ptp) REVERT: B 175 GLN cc_start: 0.7996 (mm110) cc_final: 0.7691 (mp10) REVERT: M 218 ASP cc_start: 0.7489 (t0) cc_final: 0.7220 (p0) REVERT: M 283 MET cc_start: 0.8206 (tpp) cc_final: 0.7879 (tpp) REVERT: F 354 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7369 (m-80) outliers start: 30 outliers final: 25 residues processed: 158 average time/residue: 0.1056 time to fit residues: 24.8871 Evaluate side-chains 158 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 293 VAL Chi-restraints excluded: chain M residue 332 CYS Chi-restraints excluded: chain F residue 354 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 80 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 137 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 71 optimal weight: 0.0050 chunk 12 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.200567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.159038 restraints weight = 12122.229| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.59 r_work: 0.3117 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12036 Z= 0.106 Angle : 0.475 8.171 16385 Z= 0.247 Chirality : 0.038 0.142 1911 Planarity : 0.003 0.039 1969 Dihedral : 4.882 54.311 1694 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.29 % Allowed : 11.87 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.22), residues: 1428 helix: 3.09 (0.19), residues: 664 sheet: 0.18 (0.29), residues: 288 loop : -0.52 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 98 TYR 0.019 0.001 TYR E 94 PHE 0.013 0.001 PHE R 154 TRP 0.021 0.001 TRP B 82 HIS 0.002 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (12033) covalent geometry : angle 0.47465 / 0.25 (16379) SS BOND : bond 0.00432 / 0.21 ( 3) SS BOND : angle 1.00040 / 0.51 ( 6) hydrogen bonds : bond 0.03779 / 2.55 ( 698) hydrogen bonds : angle 4.17512 / 3.10 ( 2040) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.472 Fit side-chains REVERT: R 90 LEU cc_start: 0.8805 (tp) cc_final: 0.8600 (tp) REVERT: R 212 TYR cc_start: 0.7864 (m-80) cc_final: 0.7530 (m-80) REVERT: R 310 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.7005 (tp) REVERT: A 240 MET cc_start: 0.4939 (OUTLIER) cc_final: 0.4409 (mtm) REVERT: A 309 ASP cc_start: 0.7597 (m-30) cc_final: 0.7374 (m-30) REVERT: A 316 THR cc_start: 0.8493 (OUTLIER) cc_final: 0.8099 (p) REVERT: A 350 ASP cc_start: 0.8265 (t0) cc_final: 0.7733 (m-30) REVERT: B 101 MET cc_start: 0.9211 (mtm) cc_final: 0.8959 (ptp) REVERT: B 175 GLN cc_start: 0.7765 (mm110) cc_final: 0.7378 (mp10) REVERT: E 141 MET cc_start: 0.7897 (mmm) cc_final: 0.6881 (mmm) REVERT: M 67 MET cc_start: 0.5525 (tpt) cc_final: 0.5324 (tpp) REVERT: M 218 ASP cc_start: 0.7308 (t0) cc_final: 0.6847 (p0) REVERT: M 283 MET cc_start: 0.7949 (tpp) cc_final: 0.7558 (tpp) REVERT: F 354 PHE cc_start: 0.7801 (OUTLIER) cc_final: 0.6946 (m-80) outliers start: 29 outliers final: 24 residues processed: 160 average time/residue: 0.1099 time to fit residues: 25.8803 Evaluate side-chains 161 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 164 SER Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain M residue 293 VAL Chi-restraints excluded: chain M residue 332 CYS Chi-restraints excluded: chain F residue 354 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 124 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 53 optimal weight: 0.0970 chunk 44 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 76 optimal weight: 0.0170 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 330 ASN ** M 106 ASN ** 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 = 0.4208 r_free = 0.4208 target = 0.202012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.173327 restraints weight = 12144.055| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 1.31 r_work: 0.3499 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12036 Z= 0.099 Angle : 0.467 8.142 16385 Z= 0.242 Chirality : 0.038 0.142 1911 Planarity : 0.003 0.038 1969 Dihedral : 4.727 56.551 1694 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.29 % Allowed : 12.10 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.22), residues: 1428 helix: 3.19 (0.19), residues: 664 sheet: 0.33 (0.30), residues: 279 loop : -0.52 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 98 TYR 0.015 0.001 TYR E 94 PHE 0.012 0.001 PHE R 154 TRP 0.021 0.001 TRP B 82 HIS 0.002 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (12033) covalent geometry : angle 0.46689 / 0.24 (16379) SS BOND : bond 0.00432 / 0.21 ( 3) SS BOND : angle 1.00670 / 0.51 ( 6) hydrogen bonds : bond 0.03560 / 2.40 ( 698) hydrogen bonds : angle 4.07623 / 3.03 ( 2040) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3292.05 seconds wall clock time: 57 minutes 18.92 seconds (3438.92 seconds total)