Starting phenix.real_space_refine on Wed Mar 4 23:45:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wkd_32565/03_2026/7wkd_32565.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wkd_32565/03_2026/7wkd_32565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wkd_32565/03_2026/7wkd_32565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wkd_32565/03_2026/7wkd_32565.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wkd_32565/03_2026/7wkd_32565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wkd_32565/03_2026/7wkd_32565.map" } resolution = 3.01 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= 0.002 sd= 0.033 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 63 5.16 5 C 5610 2.51 5 N 1504 2.21 5 O 1626 1.98 5 H 8727 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17530 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3794 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 5103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5103 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 3479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3479 Classifications: {'peptide': 230} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 2 Chain: "G" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 827 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "R" Number of atoms: 4279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 4279 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 3.22, per 1000 atoms: 0.18 Number of scatterers: 17530 At special positions: 0 Unit cell: (121.68, 89.44, 123.76, 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 63 16.00 O 1626 8.00 N 1504 7.00 C 5610 6.00 H 8727 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 598.3 milliseconds 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 38.0% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.782A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 248 through 252 removed outlier: 4.454A pdb=" N THR A 251 " --> pdb=" O TRP A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 298 through 318 Processing helix chain 'A' and resid 338 through 358 removed outlier: 3.584A pdb=" N ASP A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 30 Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.987A pdb=" N ILE B 38 " --> pdb=" O THR B 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 55 Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.563A pdb=" N THR E 90 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 28 through 43 removed outlier: 3.731A pdb=" N ALA G 32 " --> pdb=" O LYS G 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 52 Processing helix chain 'R' and resid 58 through 89 removed outlier: 3.580A pdb=" N MET R 73 " --> pdb=" O VAL R 69 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU R 80 " --> pdb=" O VAL R 76 " (cutoff:3.500A) Proline residue: R 81 - end of helix Processing helix chain 'R' and resid 93 through 129 removed outlier: 3.593A pdb=" N SER R 113 " --> pdb=" O ILE R 109 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 137 removed outlier: 3.669A pdb=" N PHE R 135 " --> pdb=" O ILE R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 158 Processing helix chain 'R' and resid 158 through 163 removed outlier: 4.088A pdb=" N PHE R 162 " --> pdb=" O MET R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 184 through 187 Processing helix chain 'R' and resid 188 through 198 Processing helix chain 'R' and resid 200 through 220 Processing helix chain 'R' and resid 263 through 290 Proline residue: R 281 - end of helix removed outlier: 3.672A pdb=" N VAL R 287 " --> pdb=" O ARG R 283 " (cutoff:3.500A) Processing helix chain 'R' and resid 298 through 320 Proline residue: R 317 - end of helix Processing helix chain 'R' and resid 324 through 335 removed outlier: 3.512A pdb=" N ARG R 328 " --> pdb=" O SER R 324 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.563A pdb=" N LEU A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N PHE A 199 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N VAL A 254 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N HIS A 329 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU A 256 " --> pdb=" O HIS A 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56 removed outlier: 5.236A pdb=" N THR B 52 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASN B 345 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B 341 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 6.463A pdb=" N ALA B 78 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N MET B 66 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL B 76 " --> pdb=" O MET B 66 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N TRP B 68 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N LEU B 74 " --> pdb=" O TRP B 68 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ASP B 88 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LYS B 94 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.879A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLY B 121 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ILE B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 7.007A pdb=" N SER B 165 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N CYS B 154 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL B 163 " --> pdb=" O CYS B 154 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N PHE B 156 " --> pdb=" O GLN B 161 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N GLN B 161 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N CYS B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N THR B 184 " --> pdb=" O CYS B 171 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU B 173 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN B 180 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 7.095A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 3.932A pdb=" N SER B 250 " --> pdb=" O THR B 254 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N THR B 254 " --> pdb=" O SER B 250 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N CYS B 255 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR B 268 " --> pdb=" O CYS B 255 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU B 257 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN B 264 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 3.584A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.017A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.017A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE E 109 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.064A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 165 through 166 removed outlier: 3.732A pdb=" N ASP R 165 " --> pdb=" O GLY R 180 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1260 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: 4.52 Time building geometry restraints manager: 2.26 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: 8677 1.03 - 1.23: 55 1.23 - 1.42: 3814 1.42 - 1.62: 5072 1.62 - 1.81: 94 Bond restraints: 17712 Sorted by residual: bond pdb=" CA PCA C 1 " pdb=" CB PCA C 1 " ideal model delta sigma weight residual 1.530 1.224 0.306 2.00e-02 2.50e+03 2.33e+02 bond pdb=" N LPD C 3 " pdb=" CA LPD C 3 " ideal model delta sigma weight residual 1.466 1.686 -0.220 1.50e-02 4.44e+03 2.15e+02 bond pdb=" CG PCA C 1 " pdb=" CD PCA C 1 " ideal model delta sigma weight residual 1.517 1.282 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C PCA C 1 " pdb=" N HIS C 2 " ideal model delta sigma weight residual 1.329 1.486 -0.157 1.40e-02 5.10e+03 1.26e+02 bond pdb=" N LPD C 3 " pdb=" CD LPD C 3 " ideal model delta sigma weight residual 1.473 1.322 0.151 1.40e-02 5.10e+03 1.17e+02 ... (remaining 17707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 31792 2.67 - 5.35: 60 5.35 - 8.02: 4 8.02 - 10.69: 1 10.69 - 13.37: 1 Bond angle restraints: 31858 Sorted by residual: angle pdb=" CA PCA C 1 " pdb=" N PCA C 1 " pdb=" H PCA C 1 " ideal model delta sigma weight residual 114.00 127.37 -13.37 3.00e+00 1.11e-01 1.99e+01 angle pdb=" CB HIS C 2 " pdb=" CG HIS C 2 " pdb=" CD2 HIS C 2 " ideal model delta sigma weight residual 131.20 126.08 5.12 1.30e+00 5.92e-01 1.55e+01 angle pdb=" N PCA C 1 " pdb=" CA PCA C 1 " pdb=" CB PCA C 1 " ideal model delta sigma weight residual 110.50 104.42 6.08 1.70e+00 3.46e-01 1.28e+01 angle pdb=" CA PCA C 1 " pdb=" N PCA C 1 " pdb=" CD PCA C 1 " ideal model delta sigma weight residual 114.17 105.29 8.88 3.00e+00 1.11e-01 8.76e+00 angle pdb=" N LPD C 3 " pdb=" CA LPD C 3 " pdb=" CB LPD C 3 " ideal model delta sigma weight residual 103.00 106.04 -3.04 1.10e+00 8.26e-01 7.62e+00 ... (remaining 31853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.93: 8172 26.93 - 53.86: 145 53.86 - 80.79: 41 80.79 - 107.72: 2 107.72 - 134.65: 1 Dihedral angle restraints: 8361 sinusoidal: 4471 harmonic: 3890 Sorted by residual: dihedral pdb=" N LPD C 3 " pdb=" CA LPD C 3 " pdb=" CB LPD C 3 " pdb=" HB3 LPD C 3 " ideal model delta sinusoidal sigma weight residual 279.27 144.62 134.65 1 3.00e+01 1.11e-03 1.82e+01 dihedral pdb=" N LPD C 3 " pdb=" CA LPD C 3 " pdb=" CB LPD C 3 " pdb=" HB2 LPD C 3 " ideal model delta sinusoidal sigma weight residual 159.47 -93.22 -107.31 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" N PCA C 1 " pdb=" C PCA C 1 " pdb=" CA PCA C 1 " pdb=" CB PCA C 1 " ideal model delta harmonic sigma weight residual 122.80 114.78 8.02 0 2.50e+00 1.60e-01 1.03e+01 ... (remaining 8358 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 912 0.028 - 0.055: 302 0.055 - 0.083: 87 0.083 - 0.110: 50 0.110 - 0.138: 30 Chirality restraints: 1381 Sorted by residual: chirality pdb=" CA HIS C 2 " pdb=" N HIS C 2 " pdb=" C HIS C 2 " pdb=" CB HIS C 2 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA ILE B 86 " pdb=" N ILE B 86 " pdb=" C ILE B 86 " pdb=" CB ILE B 86 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA VAL E 199 " pdb=" N VAL E 199 " pdb=" C VAL E 199 " pdb=" CB VAL E 199 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 1378 not shown) Planarity restraints: 2612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 73 " -0.015 5.00e-02 4.00e+02 2.20e-02 7.77e-01 pdb=" N PRO E 74 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO E 74 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO E 74 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 240 " 0.014 5.00e-02 4.00e+02 2.06e-02 6.77e-01 pdb=" N PRO B 241 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO B 241 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO B 241 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 98 " -0.013 5.00e-02 4.00e+02 1.92e-02 5.92e-01 pdb=" N PRO B 99 " 0.033 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " -0.011 5.00e-02 4.00e+02 ... (remaining 2609 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1498 2.23 - 2.83: 40190 2.83 - 3.42: 46760 3.42 - 4.01: 64054 4.01 - 4.60: 98630 Nonbonded interactions: 251132 Sorted by model distance: nonbonded pdb=" O THR G 5 " pdb=" H ALA G 9 " model vdw 1.643 2.450 nonbonded pdb=" HE2 HIS B 316 " pdb=" OG1 THR B 334 " model vdw 1.654 2.450 nonbonded pdb="HD22 ASN E 169 " pdb=" OH TYR E 173 " model vdw 1.665 2.450 nonbonded pdb=" H ARG E 86 " pdb=" OD2 ASP E 89 " model vdw 1.669 2.450 nonbonded pdb=" HG SER B 79 " pdb=" OD1 ASP B 81 " model vdw 1.672 2.450 ... (remaining 251127 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.890 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 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 : 0.007 0.306 8985 Z= 0.410 Angle : 0.408 8.882 12171 Z= 0.235 Chirality : 0.037 0.138 1381 Planarity : 0.002 0.022 1536 Dihedral : 7.824 81.535 3230 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.31 % Allowed : 2.92 % Favored : 96.77 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.23), residues: 1097 helix: 0.04 (0.25), residues: 385 sheet: -1.34 (0.30), residues: 251 loop : -1.95 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 57 TYR 0.004 0.000 TYR E 228 PHE 0.007 0.001 PHE A 189 TRP 0.008 0.001 TRP B 87 HIS 0.001 0.000 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00722 ( 8985) covalent geometry : angle 0.40812 (12171) hydrogen bonds : bond 0.13116 ( 443) hydrogen bonds : angle 6.31725 ( 1260) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Evaluate side-chains 345 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 342 time to evaluate : 0.460 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 LYS cc_start: 0.7974 (tptt) cc_final: 0.7770 (tptt) REVERT: A 276 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6779 (tm-30) REVERT: B 35 LEU cc_start: 0.6859 (tp) cc_final: 0.6623 (tt) REVERT: B 133 THR cc_start: 0.8063 (p) cc_final: 0.7725 (t) REVERT: B 203 LEU cc_start: 0.7683 (mt) cc_final: 0.7442 (mp) REVERT: B 239 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7244 (t80) REVERT: B 244 ASN cc_start: 0.7569 (m-40) cc_final: 0.7339 (m110) REVERT: B 251 ASP cc_start: 0.5791 (p0) cc_final: 0.5281 (p0) REVERT: B 252 ASP cc_start: 0.5060 (t0) cc_final: 0.4729 (t0) REVERT: E 167 HIS cc_start: 0.7542 (t70) cc_final: 0.7304 (t-90) REVERT: G 47 ASP cc_start: 0.7390 (t0) cc_final: 0.7088 (t0) REVERT: R 131 ILE cc_start: 0.7288 (mm) cc_final: 0.7065 (mm) REVERT: R 263 GLN cc_start: 0.5627 (pm20) cc_final: 0.4815 (pm20) REVERT: R 319 ILE cc_start: 0.7600 (tp) cc_final: 0.7217 (pt) outliers start: 3 outliers final: 0 residues processed: 344 average time/residue: 0.2325 time to fit residues: 107.9523 Evaluate side-chains 299 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 298 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.0980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.4980 chunk 106 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN B 300 ASN ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 105 GLN R 297 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.153276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.140974 restraints weight = 36652.636| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 1.94 r_work: 0.3772 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8985 Z= 0.121 Angle : 0.468 5.425 12171 Z= 0.246 Chirality : 0.038 0.166 1381 Planarity : 0.004 0.035 1536 Dihedral : 3.404 58.509 1227 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.46 % Allowed : 11.05 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.25), residues: 1097 helix: 1.36 (0.27), residues: 384 sheet: -1.14 (0.30), residues: 248 loop : -1.35 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 224 TYR 0.014 0.001 TYR A 306 PHE 0.009 0.001 PHE B 240 TRP 0.008 0.001 TRP A 248 HIS 0.010 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 8985) covalent geometry : angle 0.46761 (12171) hydrogen bonds : bond 0.03145 ( 443) hydrogen bonds : angle 4.92381 ( 1260) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Evaluate side-chains 326 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 312 time to evaluate : 0.484 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 VAL cc_start: 0.8423 (t) cc_final: 0.8188 (p) REVERT: A 193 LYS cc_start: 0.8239 (tptt) cc_final: 0.7917 (tptt) REVERT: A 198 MET cc_start: 0.8315 (ttp) cc_final: 0.8049 (ttm) REVERT: A 276 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7456 (tm-30) REVERT: B 35 LEU cc_start: 0.6761 (tp) cc_final: 0.6544 (tt) REVERT: B 62 LYS cc_start: 0.8185 (mtmt) cc_final: 0.7943 (mtmm) REVERT: B 81 ASP cc_start: 0.7155 (p0) cc_final: 0.6883 (p0) REVERT: B 88 ASP cc_start: 0.7674 (t0) cc_final: 0.7357 (t0) REVERT: B 123 ASP cc_start: 0.7630 (t0) cc_final: 0.7087 (t0) REVERT: B 129 TYR cc_start: 0.7344 (m-80) cc_final: 0.6513 (m-80) REVERT: B 194 SER cc_start: 0.8080 (p) cc_final: 0.7838 (t) REVERT: B 203 LEU cc_start: 0.8027 (mt) cc_final: 0.7810 (mp) REVERT: B 239 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7269 (t80) REVERT: B 244 ASN cc_start: 0.7999 (m-40) cc_final: 0.7770 (m110) REVERT: B 259 ASP cc_start: 0.7340 (t70) cc_final: 0.7072 (t0) REVERT: E 167 HIS cc_start: 0.7870 (t70) cc_final: 0.7487 (t-90) REVERT: E 204 SER cc_start: 0.8599 (t) cc_final: 0.8258 (p) REVERT: G 47 ASP cc_start: 0.7750 (t0) cc_final: 0.7434 (t0) REVERT: R 263 GLN cc_start: 0.6316 (pm20) cc_final: 0.5397 (pm20) outliers start: 14 outliers final: 10 residues processed: 321 average time/residue: 0.2520 time to fit residues: 108.0317 Evaluate side-chains 310 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 299 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 344 TRP Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 324 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 82 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 106 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 216 ASN A 324 HIS A 329 HIS A 344 ASN A 359 ASN B 130 ASN ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.133642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.119739 restraints weight = 37191.664| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.92 r_work: 0.3507 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 8985 Z= 0.305 Angle : 0.635 5.806 12171 Z= 0.343 Chirality : 0.043 0.243 1381 Planarity : 0.005 0.055 1536 Dihedral : 4.521 57.724 1227 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.44 % Allowed : 13.24 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.25), residues: 1097 helix: 1.29 (0.26), residues: 383 sheet: -1.24 (0.30), residues: 251 loop : -0.86 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 224 TYR 0.023 0.003 TYR E 190 PHE 0.025 0.003 PHE B 240 TRP 0.021 0.002 TRP R 160 HIS 0.010 0.003 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00665 ( 8985) covalent geometry : angle 0.63472 (12171) hydrogen bonds : bond 0.04175 ( 443) hydrogen bonds : angle 5.24006 ( 1260) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Evaluate side-chains 345 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 312 time to evaluate : 0.479 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 VAL cc_start: 0.8419 (t) cc_final: 0.8166 (p) REVERT: A 31 ARG cc_start: 0.7684 (mtm110) cc_final: 0.7296 (mtm110) REVERT: A 193 LYS cc_start: 0.8314 (tptt) cc_final: 0.8100 (tptt) REVERT: A 216 ASN cc_start: 0.7571 (m-40) cc_final: 0.7337 (m-40) REVERT: A 276 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7776 (tm-30) REVERT: A 298 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7292 (t0) REVERT: B 53 ARG cc_start: 0.8264 (mmt180) cc_final: 0.8051 (mmp80) REVERT: B 63 ILE cc_start: 0.8867 (mt) cc_final: 0.8644 (mm) REVERT: B 123 ASP cc_start: 0.7742 (t0) cc_final: 0.7226 (t0) REVERT: B 129 TYR cc_start: 0.8418 (m-80) cc_final: 0.7322 (m-80) REVERT: B 142 ARG cc_start: 0.7891 (tpp-160) cc_final: 0.7684 (tpp-160) REVERT: B 178 THR cc_start: 0.8131 (m) cc_final: 0.7914 (p) REVERT: B 235 ASN cc_start: 0.7607 (m-40) cc_final: 0.7382 (m-40) REVERT: B 244 ASN cc_start: 0.8113 (m-40) cc_final: 0.7764 (m-40) REVERT: B 321 SER cc_start: 0.8010 (t) cc_final: 0.7641 (p) REVERT: E 66 ARG cc_start: 0.8480 (mtm110) cc_final: 0.8254 (mtm110) REVERT: E 167 HIS cc_start: 0.8184 (t70) cc_final: 0.7776 (t-90) REVERT: E 220 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7372 (mm-30) REVERT: R 298 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7258 (mm-30) outliers start: 33 outliers final: 19 residues processed: 324 average time/residue: 0.2623 time to fit residues: 111.5550 Evaluate side-chains 305 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 285 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 324 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 107 optimal weight: 0.4980 chunk 106 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 329 HIS B 130 ASN ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.134213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.120354 restraints weight = 37031.835| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.89 r_work: 0.3520 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8985 Z= 0.156 Angle : 0.517 5.427 12171 Z= 0.272 Chirality : 0.039 0.207 1381 Planarity : 0.004 0.034 1536 Dihedral : 4.233 59.024 1227 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.92 % Allowed : 16.58 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.26), residues: 1097 helix: 1.71 (0.27), residues: 384 sheet: -1.08 (0.30), residues: 248 loop : -0.82 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.013 0.001 TYR B 64 PHE 0.017 0.001 PHE B 204 TRP 0.008 0.001 TRP B 104 HIS 0.007 0.002 HIS B 271 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8985) covalent geometry : angle 0.51690 (12171) hydrogen bonds : bond 0.03368 ( 443) hydrogen bonds : angle 4.88341 ( 1260) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Evaluate side-chains 325 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 297 time to evaluate : 0.468 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7648 (mtm110) cc_final: 0.7250 (mtm110) REVERT: A 193 LYS cc_start: 0.8299 (tptt) cc_final: 0.8064 (tptt) REVERT: A 216 ASN cc_start: 0.7378 (m-40) cc_final: 0.7142 (m-40) REVERT: A 252 ILE cc_start: 0.8648 (mm) cc_final: 0.8266 (tt) REVERT: A 276 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7712 (tm-30) REVERT: A 341 ARG cc_start: 0.8026 (tpp-160) cc_final: 0.7764 (ttm170) REVERT: A 348 ASP cc_start: 0.7901 (t70) cc_final: 0.7442 (t0) REVERT: B 63 ILE cc_start: 0.8833 (mt) cc_final: 0.8574 (mt) REVERT: B 123 ASP cc_start: 0.7677 (t0) cc_final: 0.7093 (t0) REVERT: B 129 TYR cc_start: 0.8370 (m-80) cc_final: 0.7636 (m-80) REVERT: B 169 THR cc_start: 0.8344 (p) cc_final: 0.8056 (m) REVERT: B 178 THR cc_start: 0.8142 (m) cc_final: 0.7926 (p) REVERT: B 235 ASN cc_start: 0.7609 (m-40) cc_final: 0.7240 (m-40) REVERT: B 251 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7703 (m-30) REVERT: B 321 SER cc_start: 0.7811 (t) cc_final: 0.7531 (p) REVERT: E 10 LEU cc_start: 0.8512 (tt) cc_final: 0.8304 (tt) REVERT: E 56 THR cc_start: 0.8320 (p) cc_final: 0.8016 (p) REVERT: E 66 ARG cc_start: 0.8479 (mtm110) cc_final: 0.8211 (mtm110) REVERT: E 220 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7392 (mm-30) REVERT: R 298 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7202 (mm-30) outliers start: 28 outliers final: 18 residues processed: 307 average time/residue: 0.2710 time to fit residues: 109.0537 Evaluate side-chains 312 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 293 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 82 ASN Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 201 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 66 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 ASN R 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.129588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.115765 restraints weight = 37100.587| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.86 r_work: 0.3453 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.5745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 8985 Z= 0.308 Angle : 0.579 5.065 12171 Z= 0.315 Chirality : 0.042 0.236 1381 Planarity : 0.005 0.053 1536 Dihedral : 4.610 59.085 1227 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.02 % Allowed : 18.25 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.25), residues: 1097 helix: 1.33 (0.27), residues: 384 sheet: -0.97 (0.30), residues: 257 loop : -0.74 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 71 TYR 0.019 0.002 TYR E 190 PHE 0.025 0.002 PHE B 240 TRP 0.011 0.002 TRP R 160 HIS 0.010 0.002 HIS E 232 Details of bonding type rmsd covalent geometry : bond 0.00670 ( 8985) covalent geometry : angle 0.57943 (12171) hydrogen bonds : bond 0.03947 ( 443) hydrogen bonds : angle 5.16055 ( 1260) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Evaluate side-chains 341 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 312 time to evaluate : 0.494 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7744 (mtm110) cc_final: 0.7321 (mtm110) REVERT: A 193 LYS cc_start: 0.8287 (tptt) cc_final: 0.8053 (tptt) REVERT: A 276 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7721 (tm-30) REVERT: B 53 ARG cc_start: 0.8320 (mmt180) cc_final: 0.8117 (mmp80) REVERT: B 63 ILE cc_start: 0.8879 (mt) cc_final: 0.8629 (mt) REVERT: B 102 SER cc_start: 0.8214 (t) cc_final: 0.7730 (p) REVERT: B 123 ASP cc_start: 0.7800 (t0) cc_final: 0.7210 (t0) REVERT: B 169 THR cc_start: 0.8366 (p) cc_final: 0.8060 (m) REVERT: B 251 ASP cc_start: 0.8188 (m-30) cc_final: 0.7936 (m-30) REVERT: B 321 SER cc_start: 0.7941 (t) cc_final: 0.7636 (p) REVERT: E 11 VAL cc_start: 0.8490 (t) cc_final: 0.8241 (m) REVERT: E 167 HIS cc_start: 0.8287 (t70) cc_final: 0.7851 (t-90) REVERT: E 220 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7483 (mm-30) REVERT: R 106 TYR cc_start: 0.7687 (m-80) cc_final: 0.7459 (m-10) REVERT: R 107 LEU cc_start: 0.7487 (tp) cc_final: 0.7250 (tp) REVERT: R 187 TYR cc_start: 0.7100 (m-80) cc_final: 0.6876 (m-80) REVERT: R 267 MET cc_start: 0.7887 (tpt) cc_final: 0.7509 (tpp) REVERT: R 298 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7304 (mm-30) REVERT: R 312 ASN cc_start: 0.8294 (t0) cc_final: 0.7974 (t0) outliers start: 29 outliers final: 23 residues processed: 320 average time/residue: 0.2816 time to fit residues: 117.1076 Evaluate side-chains 318 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 295 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 217 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 84 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN E 171 ASN ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.131036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.117238 restraints weight = 36672.032| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.85 r_work: 0.3479 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.5948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8985 Z= 0.167 Angle : 0.520 5.219 12171 Z= 0.276 Chirality : 0.040 0.209 1381 Planarity : 0.004 0.048 1536 Dihedral : 4.444 59.384 1227 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.71 % Allowed : 20.75 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.26), residues: 1097 helix: 1.58 (0.27), residues: 384 sheet: -0.89 (0.30), residues: 248 loop : -0.64 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 54 TYR 0.013 0.002 TYR E 58 PHE 0.013 0.001 PHE B 240 TRP 0.008 0.001 TRP E 110 HIS 0.005 0.001 HIS B 271 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8985) covalent geometry : angle 0.51970 (12171) hydrogen bonds : bond 0.03502 ( 443) hydrogen bonds : angle 4.92705 ( 1260) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Evaluate side-chains 331 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 305 time to evaluate : 0.533 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 SER cc_start: 0.7784 (OUTLIER) cc_final: 0.7556 (t) REVERT: A 10 LYS cc_start: 0.8148 (mtmm) cc_final: 0.7865 (mttm) REVERT: A 29 VAL cc_start: 0.8356 (t) cc_final: 0.8084 (p) REVERT: A 31 ARG cc_start: 0.7681 (mtm110) cc_final: 0.7258 (mtm110) REVERT: A 33 THR cc_start: 0.8545 (t) cc_final: 0.8238 (p) REVERT: A 193 LYS cc_start: 0.8281 (tptt) cc_final: 0.8054 (tptt) REVERT: A 248 TRP cc_start: 0.8588 (m100) cc_final: 0.8219 (m100) REVERT: A 276 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7732 (tm-30) REVERT: A 341 ARG cc_start: 0.8029 (tpp-160) cc_final: 0.7579 (tpp80) REVERT: B 53 ARG cc_start: 0.8348 (mmt180) cc_final: 0.8147 (mmp80) REVERT: B 63 ILE cc_start: 0.8865 (mt) cc_final: 0.8610 (mt) REVERT: B 102 SER cc_start: 0.8215 (t) cc_final: 0.7730 (p) REVERT: B 123 ASP cc_start: 0.7699 (t0) cc_final: 0.7127 (t0) REVERT: B 129 TYR cc_start: 0.8438 (m-80) cc_final: 0.7735 (m-80) REVERT: B 321 SER cc_start: 0.7845 (t) cc_final: 0.7521 (p) REVERT: B 322 CYS cc_start: 0.7781 (p) cc_final: 0.7499 (p) REVERT: E 220 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7461 (mm-30) REVERT: R 106 TYR cc_start: 0.7683 (m-80) cc_final: 0.7397 (m-10) REVERT: R 107 LEU cc_start: 0.7468 (tp) cc_final: 0.7224 (tp) REVERT: R 267 MET cc_start: 0.7816 (tpt) cc_final: 0.7475 (tpp) REVERT: R 298 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7332 (mm-30) REVERT: R 327 PHE cc_start: 0.7993 (t80) cc_final: 0.7704 (t80) outliers start: 26 outliers final: 21 residues processed: 317 average time/residue: 0.2774 time to fit residues: 114.9999 Evaluate side-chains 317 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 295 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 145 ILE Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 217 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 89 optimal weight: 0.6980 chunk 71 optimal weight: 0.0870 chunk 70 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 ASN ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN E 171 ASN G 58 ASN ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.129730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.115891 restraints weight = 37067.285| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.86 r_work: 0.3457 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.6225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8985 Z= 0.233 Angle : 0.543 5.070 12171 Z= 0.292 Chirality : 0.041 0.220 1381 Planarity : 0.004 0.046 1536 Dihedral : 4.553 59.443 1227 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.02 % Allowed : 20.02 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.26), residues: 1097 helix: 1.50 (0.27), residues: 384 sheet: -0.93 (0.29), residues: 258 loop : -0.60 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 54 TYR 0.014 0.002 TYR E 190 PHE 0.020 0.002 PHE B 240 TRP 0.013 0.002 TRP R 91 HIS 0.006 0.001 HIS C 2 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 8985) covalent geometry : angle 0.54322 (12171) hydrogen bonds : bond 0.03645 ( 443) hydrogen bonds : angle 4.98623 ( 1260) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Evaluate side-chains 337 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 308 time to evaluate : 0.495 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8169 (mtmm) cc_final: 0.7907 (mttm) REVERT: A 29 VAL cc_start: 0.8354 (t) cc_final: 0.8072 (p) REVERT: A 33 THR cc_start: 0.8544 (t) cc_final: 0.8228 (p) REVERT: A 185 PHE cc_start: 0.7690 (t80) cc_final: 0.7273 (t80) REVERT: A 193 LYS cc_start: 0.8283 (tptt) cc_final: 0.8070 (tptt) REVERT: A 248 TRP cc_start: 0.8639 (m100) cc_final: 0.7981 (m100) REVERT: A 276 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7739 (tm-30) REVERT: A 341 ARG cc_start: 0.8063 (tpp-160) cc_final: 0.7710 (mtt180) REVERT: B 53 ARG cc_start: 0.8362 (mmt180) cc_final: 0.8146 (mmp80) REVERT: B 56 LEU cc_start: 0.8335 (mt) cc_final: 0.8130 (mp) REVERT: B 63 ILE cc_start: 0.8892 (mt) cc_final: 0.8622 (mt) REVERT: B 102 SER cc_start: 0.8219 (t) cc_final: 0.7751 (p) REVERT: B 123 ASP cc_start: 0.7855 (t0) cc_final: 0.7274 (t0) REVERT: B 129 TYR cc_start: 0.8449 (m-80) cc_final: 0.7952 (m-80) REVERT: B 142 ARG cc_start: 0.7880 (tpp-160) cc_final: 0.7618 (tpp-160) REVERT: B 321 SER cc_start: 0.7897 (t) cc_final: 0.7573 (p) REVERT: E 220 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7467 (mm-30) REVERT: G 40 CYS cc_start: 0.7363 (m) cc_final: 0.7137 (m) REVERT: R 106 TYR cc_start: 0.7695 (m-80) cc_final: 0.7422 (m-10) REVERT: R 187 TYR cc_start: 0.7126 (m-80) cc_final: 0.6833 (m-80) REVERT: R 267 MET cc_start: 0.7850 (tpt) cc_final: 0.7500 (tpp) REVERT: R 277 LEU cc_start: 0.8051 (mt) cc_final: 0.7824 (mm) REVERT: R 298 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7276 (mm-30) REVERT: R 327 PHE cc_start: 0.7999 (t80) cc_final: 0.7725 (t80) outliers start: 29 outliers final: 24 residues processed: 317 average time/residue: 0.2651 time to fit residues: 110.0310 Evaluate side-chains 327 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 303 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 145 ILE Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 217 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 83 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 297 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.131629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.118051 restraints weight = 36736.567| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.84 r_work: 0.3470 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.6277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8985 Z= 0.153 Angle : 0.512 5.127 12171 Z= 0.273 Chirality : 0.040 0.204 1381 Planarity : 0.004 0.041 1536 Dihedral : 4.447 59.469 1227 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.61 % Allowed : 20.33 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.26), residues: 1097 helix: 1.68 (0.27), residues: 384 sheet: -0.94 (0.29), residues: 266 loop : -0.44 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 54 TYR 0.011 0.001 TYR E 190 PHE 0.011 0.001 PHE B 240 TRP 0.010 0.001 TRP B 344 HIS 0.004 0.001 HIS C 2 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8985) covalent geometry : angle 0.51162 (12171) hydrogen bonds : bond 0.03403 ( 443) hydrogen bonds : angle 4.86103 ( 1260) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Evaluate side-chains 324 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 299 time to evaluate : 0.513 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8143 (mtmm) cc_final: 0.7871 (mttm) REVERT: A 29 VAL cc_start: 0.8345 (t) cc_final: 0.8082 (p) REVERT: A 31 ARG cc_start: 0.7700 (mtm110) cc_final: 0.7305 (mtm110) REVERT: A 33 THR cc_start: 0.8551 (t) cc_final: 0.8245 (p) REVERT: A 39 LEU cc_start: 0.7791 (mt) cc_final: 0.7518 (mt) REVERT: A 185 PHE cc_start: 0.7675 (t80) cc_final: 0.7293 (t80) REVERT: A 193 LYS cc_start: 0.8277 (tptt) cc_final: 0.8057 (tptt) REVERT: A 248 TRP cc_start: 0.8530 (m100) cc_final: 0.8293 (m100) REVERT: A 276 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7737 (tm-30) REVERT: A 341 ARG cc_start: 0.8121 (tpp-160) cc_final: 0.7775 (mtt180) REVERT: B 63 ILE cc_start: 0.8867 (mt) cc_final: 0.8573 (mt) REVERT: B 102 SER cc_start: 0.8205 (t) cc_final: 0.7736 (p) REVERT: B 123 ASP cc_start: 0.7748 (t0) cc_final: 0.7166 (t0) REVERT: B 129 TYR cc_start: 0.8390 (m-80) cc_final: 0.7821 (m-80) REVERT: B 142 ARG cc_start: 0.7904 (tpp-160) cc_final: 0.7654 (tpp-160) REVERT: B 321 SER cc_start: 0.7887 (t) cc_final: 0.7551 (p) REVERT: E 220 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7486 (mm-30) REVERT: R 267 MET cc_start: 0.7850 (tpt) cc_final: 0.7480 (tpp) REVERT: R 277 LEU cc_start: 0.8032 (mt) cc_final: 0.7804 (mm) REVERT: R 298 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7269 (mm-30) REVERT: R 327 PHE cc_start: 0.7985 (t80) cc_final: 0.7713 (t80) outliers start: 25 outliers final: 19 residues processed: 309 average time/residue: 0.2673 time to fit residues: 108.1653 Evaluate side-chains 315 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 296 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 82 ASN Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 217 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 76 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 25 optimal weight: 0.3980 chunk 58 optimal weight: 0.6980 chunk 87 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN R 43 ASN R 297 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.131543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.117926 restraints weight = 36964.962| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.85 r_work: 0.3473 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.6357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8985 Z= 0.154 Angle : 0.510 5.050 12171 Z= 0.271 Chirality : 0.040 0.202 1381 Planarity : 0.004 0.040 1536 Dihedral : 4.414 59.593 1227 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.29 % Allowed : 20.86 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.26), residues: 1097 helix: 1.79 (0.26), residues: 384 sheet: -0.97 (0.29), residues: 262 loop : -0.41 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 54 TYR 0.011 0.001 TYR E 190 PHE 0.012 0.001 PHE B 204 TRP 0.009 0.001 TRP B 344 HIS 0.004 0.001 HIS C 2 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8985) covalent geometry : angle 0.51018 (12171) hydrogen bonds : bond 0.03368 ( 443) hydrogen bonds : angle 4.82091 ( 1260) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Evaluate side-chains 323 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 301 time to evaluate : 0.490 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 VAL cc_start: 0.8338 (t) cc_final: 0.8081 (p) REVERT: A 31 ARG cc_start: 0.7710 (mtm110) cc_final: 0.7328 (mtm110) REVERT: A 33 THR cc_start: 0.8551 (t) cc_final: 0.8247 (p) REVERT: A 39 LEU cc_start: 0.7784 (mt) cc_final: 0.7538 (mt) REVERT: A 185 PHE cc_start: 0.7700 (t80) cc_final: 0.7330 (t80) REVERT: A 193 LYS cc_start: 0.8278 (tptt) cc_final: 0.8058 (tptt) REVERT: A 248 TRP cc_start: 0.8488 (m100) cc_final: 0.8197 (m100) REVERT: A 276 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7738 (tm-30) REVERT: A 341 ARG cc_start: 0.8124 (ttp-170) cc_final: 0.7616 (mtt90) REVERT: B 63 ILE cc_start: 0.8858 (mt) cc_final: 0.8558 (mt) REVERT: B 102 SER cc_start: 0.8203 (t) cc_final: 0.7734 (p) REVERT: B 123 ASP cc_start: 0.7847 (t0) cc_final: 0.7234 (t0) REVERT: B 129 TYR cc_start: 0.8427 (m-80) cc_final: 0.7671 (m-80) REVERT: B 321 SER cc_start: 0.7883 (t) cc_final: 0.7556 (p) REVERT: E 86 ARG cc_start: 0.8169 (ptp-170) cc_final: 0.7885 (mtm-85) REVERT: E 220 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7497 (mm-30) REVERT: R 106 TYR cc_start: 0.7712 (m-80) cc_final: 0.7460 (m-10) REVERT: R 204 MET cc_start: 0.7190 (ttp) cc_final: 0.6969 (ttp) REVERT: R 267 MET cc_start: 0.7838 (tpt) cc_final: 0.7480 (tpp) REVERT: R 277 LEU cc_start: 0.8041 (mt) cc_final: 0.7809 (mm) REVERT: R 298 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7239 (mm-30) REVERT: R 327 PHE cc_start: 0.8038 (t80) cc_final: 0.7740 (t80) outliers start: 22 outliers final: 20 residues processed: 309 average time/residue: 0.2633 time to fit residues: 106.1981 Evaluate side-chains 317 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 297 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 217 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 60 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN R 297 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.130430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.116825 restraints weight = 36823.449| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.84 r_work: 0.3458 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.6532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8985 Z= 0.196 Angle : 0.534 5.296 12171 Z= 0.285 Chirality : 0.041 0.244 1381 Planarity : 0.004 0.040 1536 Dihedral : 4.526 59.526 1227 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.19 % Allowed : 21.79 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.26), residues: 1097 helix: 1.73 (0.26), residues: 384 sheet: -0.88 (0.29), residues: 266 loop : -0.34 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 54 TYR 0.012 0.002 TYR E 190 PHE 0.015 0.002 PHE B 240 TRP 0.010 0.002 TRP B 302 HIS 0.005 0.001 HIS C 2 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 8985) covalent geometry : angle 0.53387 (12171) hydrogen bonds : bond 0.03521 ( 443) hydrogen bonds : angle 4.88590 ( 1260) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue ILE 127 is missing expected H atoms. Skipping. Evaluate side-chains 325 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 304 time to evaluate : 0.457 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8169 (mtmm) cc_final: 0.7896 (mttm) REVERT: A 29 VAL cc_start: 0.8374 (t) cc_final: 0.8120 (p) REVERT: A 31 ARG cc_start: 0.7735 (mtm110) cc_final: 0.7384 (mtm110) REVERT: A 33 THR cc_start: 0.8558 (t) cc_final: 0.8233 (p) REVERT: A 39 LEU cc_start: 0.7794 (mt) cc_final: 0.7539 (mt) REVERT: A 185 PHE cc_start: 0.7701 (t80) cc_final: 0.7358 (t80) REVERT: A 193 LYS cc_start: 0.8288 (tptt) cc_final: 0.8081 (tptt) REVERT: A 276 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7753 (tm-30) REVERT: A 341 ARG cc_start: 0.8130 (ttp-170) cc_final: 0.7809 (mtt180) REVERT: B 22 GLN cc_start: 0.7331 (tm-30) cc_final: 0.6986 (tm-30) REVERT: B 57 ARG cc_start: 0.8265 (mtt-85) cc_final: 0.8013 (mtt180) REVERT: B 63 ILE cc_start: 0.8852 (mt) cc_final: 0.8567 (mt) REVERT: B 102 SER cc_start: 0.8217 (t) cc_final: 0.7756 (p) REVERT: B 123 ASP cc_start: 0.7839 (t0) cc_final: 0.7250 (t0) REVERT: B 129 TYR cc_start: 0.8498 (m-80) cc_final: 0.7813 (m-80) REVERT: B 134 ARG cc_start: 0.8040 (mmm160) cc_final: 0.7727 (mmm-85) REVERT: B 321 SER cc_start: 0.7879 (t) cc_final: 0.7526 (p) REVERT: B 322 CYS cc_start: 0.7841 (p) cc_final: 0.7611 (p) REVERT: E 86 ARG cc_start: 0.8196 (ptp-170) cc_final: 0.7939 (mtm-85) REVERT: E 220 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7475 (mm-30) REVERT: R 187 TYR cc_start: 0.7126 (m-80) cc_final: 0.6748 (m-80) REVERT: R 204 MET cc_start: 0.7202 (ttp) cc_final: 0.6988 (ttp) REVERT: R 267 MET cc_start: 0.7862 (tpt) cc_final: 0.7502 (tpp) REVERT: R 277 LEU cc_start: 0.8058 (mt) cc_final: 0.7832 (mm) REVERT: R 298 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7276 (mm-30) REVERT: R 327 PHE cc_start: 0.8040 (t80) cc_final: 0.7797 (t80) outliers start: 21 outliers final: 20 residues processed: 311 average time/residue: 0.2707 time to fit residues: 110.5490 Evaluate side-chains 320 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 300 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 82 ASN Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 217 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 70 optimal weight: 0.2980 chunk 69 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 76 optimal weight: 0.0970 chunk 24 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 107 optimal weight: 0.0980 chunk 31 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 HIS E 171 ASN R 297 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.132787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.119186 restraints weight = 36813.068| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.85 r_work: 0.3491 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.6495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8985 Z= 0.118 Angle : 0.503 5.410 12171 Z= 0.265 Chirality : 0.040 0.215 1381 Planarity : 0.004 0.039 1536 Dihedral : 4.350 59.668 1227 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.09 % Allowed : 21.69 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.26), residues: 1097 helix: 1.96 (0.26), residues: 384 sheet: -1.03 (0.28), residues: 275 loop : -0.29 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 54 TYR 0.021 0.001 TYR E 94 PHE 0.011 0.001 PHE B 204 TRP 0.014 0.001 TRP B 344 HIS 0.003 0.001 HIS B 271 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8985) covalent geometry : angle 0.50336 (12171) hydrogen bonds : bond 0.03242 ( 443) hydrogen bonds : angle 4.73839 ( 1260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5620.19 seconds wall clock time: 96 minutes 1.56 seconds (5761.56 seconds total)