Starting phenix.real_space_refine on Fri Sep 11 16:54:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pt0_20470/09_2026/6pt0_20470.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pt0_20470/09_2026/6pt0_20470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pt0_20470/09_2026/6pt0_20470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pt0_20470/09_2026/6pt0_20470.map" model { file = "/net/cci-nas-00/data/ceres_data/6pt0_20470/09_2026/6pt0_20470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pt0_20470/09_2026/6pt0_20470.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6pt0_20470/09_2026/6pt0_20470.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pt0_20470/09_2026/6pt0_20470.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 6554 2.51 5 N 1719 2.21 5 O 1887 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10232 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2319 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain: "A" Number of atoms: 2824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2824 Classifications: {'peptide': 353} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 348} Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2616 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 474 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 4, 'TRANS': 56} Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 216 Unusual residues: {'CLR': 4, 'PLM': 4, 'WI5': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Time building chain proxies: 2.03, per 1000 atoms: 0.20 Number of scatterers: 10232 At special positions: 0 Unit cell: (91.581, 120.393, 136.857, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 1887 8.00 N 1719 7.00 C 6554 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 174 " - pdb=" SG CYS R 179 " distance=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 290.4 milliseconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 42.2% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'R' and resid 29 through 61 removed outlier: 4.140A pdb=" N ALA R 37 " --> pdb=" O LYS R 33 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER R 61 " --> pdb=" O LEU R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 67 Processing helix chain 'R' and resid 67 through 96 Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 171 Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 187 through 227 removed outlier: 3.935A pdb=" N HIS R 226 " --> pdb=" O SER R 222 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLN R 227 " --> pdb=" O LEU R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 234 Processing helix chain 'R' and resid 238 through 271 removed outlier: 3.595A pdb=" N ARG R 242 " --> pdb=" O ARG R 238 " (cutoff:3.500A) Proline residue: R 260 - end of helix Processing helix chain 'R' and resid 274 through 302 removed outlier: 3.808A pdb=" N LYS R 278 " --> pdb=" O SER R 274 " (cutoff:3.500A) Proline residue: R 296 - end of helix Processing helix chain 'R' and resid 303 through 319 Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 63 through 88 removed outlier: 4.158A pdb=" N LYS A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLN A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 116 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'A' and resid 133 through 144 removed outlier: 4.088A pdb=" N PHE A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASN A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 152 through 158 removed outlier: 3.537A pdb=" N ASP A 158 " --> pdb=" O TYR A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 164 Processing helix chain 'A' and resid 170 through 179 removed outlier: 3.567A pdb=" N VAL A 174 " --> pdb=" O THR A 170 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 217 removed outlier: 3.687A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLY A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.910A pdb=" N ALA A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.509A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.788A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 352 removed outlier: 3.720A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.505A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.717A pdb=" N SER E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.911A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.504A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.696A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.892A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 114 removed outlier: 6.414A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.699A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR B 159 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 6.867A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.810A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.777A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.420A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.703A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 155 through 160 529 hydrogen bonds defined for protein. 1530 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.48 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1647 1.31 - 1.44: 2814 1.44 - 1.57: 5883 1.57 - 1.70: 1 1.70 - 1.82: 105 Bond restraints: 10450 Sorted by residual: bond pdb=" C1 WI5 R 401 " pdb=" C2 WI5 R 401 " ideal model delta sigma weight residual 1.409 1.601 -0.192 2.00e-02 2.50e+03 9.23e+01 bond pdb=" C23 WI5 R 401 " pdb=" C24 WI5 R 401 " ideal model delta sigma weight residual 1.366 1.516 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" C12 WI5 R 401 " pdb=" C13 WI5 R 401 " ideal model delta sigma weight residual 1.380 1.529 -0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" C21 WI5 R 401 " pdb=" C22 WI5 R 401 " ideal model delta sigma weight residual 1.374 1.515 -0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" C13 WI5 R 401 " pdb=" C8 WI5 R 401 " ideal model delta sigma weight residual 1.387 1.271 0.116 2.00e-02 2.50e+03 3.38e+01 ... (remaining 10445 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 13528 1.91 - 3.82: 505 3.82 - 5.73: 73 5.73 - 7.65: 34 7.65 - 9.56: 9 Bond angle restraints: 14149 Sorted by residual: angle pdb=" C LYS A 180 " pdb=" N THR A 181 " pdb=" CA THR A 181 " ideal model delta sigma weight residual 121.54 129.96 -8.42 1.91e+00 2.74e-01 1.94e+01 angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 129.68 -8.14 1.91e+00 2.74e-01 1.81e+01 angle pdb=" CA PRO R 138 " pdb=" C PRO R 138 " pdb=" N PRO R 139 " ideal model delta sigma weight residual 117.93 122.75 -4.82 1.20e+00 6.94e-01 1.61e+01 angle pdb=" C PRO E 41 " pdb=" N GLU E 42 " pdb=" CA GLU E 42 " ideal model delta sigma weight residual 121.54 128.91 -7.37 1.91e+00 2.74e-01 1.49e+01 angle pdb=" N PRO R 138 " pdb=" CA PRO R 138 " pdb=" C PRO R 138 " ideal model delta sigma weight residual 110.70 115.38 -4.68 1.22e+00 6.72e-01 1.47e+01 ... (remaining 14144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 5980 18.03 - 36.05: 178 36.05 - 54.08: 30 54.08 - 72.10: 4 72.10 - 90.13: 5 Dihedral angle restraints: 6197 sinusoidal: 2472 harmonic: 3725 Sorted by residual: dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 153.89 26.11 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA THR B 86 " pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta harmonic sigma weight residual 180.00 159.16 20.84 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA THR B 249 " pdb=" C THR B 249 " pdb=" N CYS B 250 " pdb=" CA CYS B 250 " ideal model delta harmonic sigma weight residual 180.00 162.17 17.83 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 6194 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1418 0.085 - 0.170: 155 0.170 - 0.255: 17 0.255 - 0.340: 4 0.340 - 0.425: 5 Chirality restraints: 1599 Sorted by residual: chirality pdb=" C14 CLR R 406 " pdb=" C13 CLR R 406 " pdb=" C15 CLR R 406 " pdb=" C8 CLR R 406 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" C14 CLR R 404 " pdb=" C13 CLR R 404 " pdb=" C15 CLR R 404 " pdb=" C8 CLR R 404 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" CG LEU A 23 " pdb=" CB LEU A 23 " pdb=" CD1 LEU A 23 " pdb=" CD2 LEU A 23 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 4.02e+00 ... (remaining 1596 not shown) Planarity restraints: 1761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 WI5 R 401 " -0.002 2.00e-02 2.50e+03 1.61e-02 7.13e+00 pdb=" C2 WI5 R 401 " -0.011 2.00e-02 2.50e+03 pdb=" C21 WI5 R 401 " -0.017 2.00e-02 2.50e+03 pdb=" C22 WI5 R 401 " -0.016 2.00e-02 2.50e+03 pdb=" C23 WI5 R 401 " -0.006 2.00e-02 2.50e+03 pdb=" C24 WI5 R 401 " -0.001 2.00e-02 2.50e+03 pdb=" C25 WI5 R 401 " 0.024 2.00e-02 2.50e+03 pdb=" C26 WI5 R 401 " 0.005 2.00e-02 2.50e+03 pdb=" C27 WI5 R 401 " -0.021 2.00e-02 2.50e+03 pdb=" C3 WI5 R 401 " 0.014 2.00e-02 2.50e+03 pdb=" C4 WI5 R 401 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " 0.040 5.00e-02 4.00e+02 6.07e-02 5.89e+00 pdb=" N PRO C 49 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 164 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C VAL R 164 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL R 164 " 0.013 2.00e-02 2.50e+03 pdb=" N SER R 165 " 0.011 2.00e-02 2.50e+03 ... (remaining 1758 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 964 2.76 - 3.29: 9726 3.29 - 3.83: 16743 3.83 - 4.36: 19129 4.36 - 4.90: 33559 Nonbonded interactions: 80121 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.222 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.270 3.040 nonbonded pdb=" O VAL R 164 " pdb=" OH TYR R 190 " model vdw 2.271 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 175 " model vdw 2.285 3.040 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 2.287 3.040 ... (remaining 80116 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: 0.650 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.830 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 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 : 0.006 0.192 10452 Z= 0.303 Angle : 0.908 15.716 14153 Z= 0.462 Chirality : 0.060 0.425 1599 Planarity : 0.006 0.061 1761 Dihedral : 9.766 90.128 3791 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.20), residues: 1272 helix: -1.12 (0.18), residues: 507 sheet: -1.80 (0.28), residues: 275 loop : -1.90 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 15 TYR 0.029 0.002 TYR A 74 PHE 0.020 0.002 PHE A 189 TRP 0.033 0.002 TRP E 111 HIS 0.008 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.30 (10450) covalent geometry : angle 0.88833 / 0.45 (14149) SS BOND : bond 0.00695 / 0.34 ( 2) SS BOND : angle 11.21410 / 6.02 ( 4) hydrogen bonds : bond 0.10955 / 7.44 ( 529) hydrogen bonds : angle 6.16697 / 4.44 ( 1530) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 0.363 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: R 41 THR cc_start: 0.8831 (m) cc_final: 0.8475 (p) REVERT: R 56 TYR cc_start: 0.7524 (t80) cc_final: 0.7165 (t80) REVERT: R 65 ARG cc_start: 0.7497 (ttt180) cc_final: 0.6410 (mtm110) REVERT: R 130 ASP cc_start: 0.8801 (t70) cc_final: 0.8390 (t0) REVERT: R 146 THR cc_start: 0.7719 (m) cc_final: 0.7430 (p) REVERT: A 25 GLU cc_start: 0.8201 (tt0) cc_final: 0.7974 (tp30) REVERT: A 29 LYS cc_start: 0.8405 (ttmt) cc_final: 0.7997 (tptt) REVERT: A 224 CYS cc_start: 0.7694 (m) cc_final: 0.7475 (p) REVERT: A 330 LYS cc_start: 0.8346 (mmtt) cc_final: 0.7992 (pttm) REVERT: A 333 GLN cc_start: 0.8506 (tp40) cc_final: 0.7971 (tp-100) REVERT: B 7 LEU cc_start: 0.9003 (mm) cc_final: 0.8757 (mm) REVERT: B 9 GLN cc_start: 0.9273 (mm110) cc_final: 0.8641 (tm-30) REVERT: B 10 GLU cc_start: 0.9468 (tp30) cc_final: 0.9180 (tp30) REVERT: B 32 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8474 (tm-30) REVERT: B 101 MET cc_start: 0.9139 (mtp) cc_final: 0.8812 (mtp) REVERT: B 209 LYS cc_start: 0.8673 (mttm) cc_final: 0.8327 (mttt) REVERT: B 243 THR cc_start: 0.8994 (m) cc_final: 0.8465 (p) REVERT: B 258 ASP cc_start: 0.8495 (t70) cc_final: 0.8282 (t0) REVERT: C 20 LYS cc_start: 0.9498 (ttpt) cc_final: 0.9127 (mtpp) REVERT: C 42 GLU cc_start: 0.8664 (tt0) cc_final: 0.8429 (tp30) REVERT: E 52 SER cc_start: 0.8625 (m) cc_final: 0.8084 (t) REVERT: E 73 ASP cc_start: 0.7224 (t70) cc_final: 0.6760 (t70) REVERT: E 80 PHE cc_start: 0.7823 (m-80) cc_final: 0.7555 (m-80) REVERT: E 223 ASP cc_start: 0.8605 (m-30) cc_final: 0.7126 (m-30) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.1041 time to fit residues: 49.9549 Evaluate side-chains 193 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 218 GLN ** R 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.126811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.082971 restraints weight = 20098.616| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.34 r_work: 0.3037 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 10452 Z= 0.256 Angle : 0.694 9.373 14153 Z= 0.356 Chirality : 0.045 0.188 1599 Planarity : 0.005 0.049 1761 Dihedral : 6.501 100.918 1496 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.40 % Allowed : 12.78 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.85 (0.22), residues: 1272 helix: 0.81 (0.22), residues: 510 sheet: -1.40 (0.30), residues: 271 loop : -1.45 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 96 TYR 0.018 0.002 TYR E 190 PHE 0.019 0.002 PHE A 334 TRP 0.021 0.002 TRP B 211 HIS 0.012 0.002 HIS E 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.26 (10450) covalent geometry : angle 0.69412 / 0.36 (14149) SS BOND : bond 0.00389 / 0.20 ( 2) SS BOND : angle 1.28513 / 0.69 ( 4) hydrogen bonds : bond 0.03772 / 2.51 ( 529) hydrogen bonds : angle 4.86150 / 3.50 ( 1530) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: R 26 MET cc_start: 0.6461 (OUTLIER) cc_final: 0.6010 (tpp) REVERT: R 56 TYR cc_start: 0.8060 (t80) cc_final: 0.7538 (t80) REVERT: R 65 ARG cc_start: 0.7549 (ttt180) cc_final: 0.6463 (mtm110) REVERT: R 130 ASP cc_start: 0.8933 (t70) cc_final: 0.8686 (t0) REVERT: R 207 TYR cc_start: 0.7847 (t80) cc_final: 0.7509 (t80) REVERT: R 276 GLN cc_start: 0.8872 (mm-40) cc_final: 0.8633 (pt0) REVERT: R 292 SER cc_start: 0.8973 (m) cc_final: 0.8656 (p) REVERT: A 9 ASP cc_start: 0.9050 (m-30) cc_final: 0.8830 (m-30) REVERT: A 51 LYS cc_start: 0.9222 (mttt) cc_final: 0.8994 (mmmt) REVERT: A 198 MET cc_start: 0.8360 (mtp) cc_final: 0.7954 (ttp) REVERT: A 224 CYS cc_start: 0.8921 (m) cc_final: 0.8290 (p) REVERT: A 243 MET cc_start: 0.9598 (tpp) cc_final: 0.9318 (mmm) REVERT: A 330 LYS cc_start: 0.8661 (mmtt) cc_final: 0.8254 (ptmt) REVERT: B 10 GLU cc_start: 0.9514 (tp30) cc_final: 0.9291 (tp30) REVERT: B 101 MET cc_start: 0.9351 (mtp) cc_final: 0.9036 (mtp) REVERT: B 209 LYS cc_start: 0.9106 (mttm) cc_final: 0.8811 (mttt) REVERT: B 243 THR cc_start: 0.9321 (m) cc_final: 0.8925 (p) REVERT: B 247 ASP cc_start: 0.8146 (t0) cc_final: 0.7734 (t0) REVERT: B 297 TRP cc_start: 0.9072 (m100) cc_final: 0.8205 (m100) REVERT: C 13 ARG cc_start: 0.9385 (mtt-85) cc_final: 0.8802 (ptp-110) REVERT: C 20 LYS cc_start: 0.9522 (ttpt) cc_final: 0.9122 (ptmm) REVERT: C 29 LYS cc_start: 0.8870 (mmmt) cc_final: 0.8419 (tppt) REVERT: C 32 LYS cc_start: 0.9293 (tttt) cc_final: 0.9008 (tptp) REVERT: C 42 GLU cc_start: 0.8995 (tt0) cc_final: 0.8737 (tm-30) REVERT: C 58 GLU cc_start: 0.8707 (pt0) cc_final: 0.7916 (pm20) REVERT: E 73 ASP cc_start: 0.7896 (t70) cc_final: 0.6936 (t70) REVERT: E 93 MET cc_start: 0.8782 (ttm) cc_final: 0.7990 (tpt) REVERT: E 148 PRO cc_start: 0.9044 (Cg_endo) cc_final: 0.8825 (Cg_exo) REVERT: E 220 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8199 (mp0) REVERT: E 222 GLU cc_start: 0.8065 (pm20) cc_final: 0.7764 (pm20) REVERT: E 223 ASP cc_start: 0.8479 (m-30) cc_final: 0.6956 (m-30) outliers start: 37 outliers final: 19 residues processed: 209 average time/residue: 0.0892 time to fit residues: 26.4592 Evaluate side-chains 178 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 26 MET Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 267 HIS Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 69 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 2 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 57 optimal weight: 0.0570 chunk 116 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 239 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.126935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.082984 restraints weight = 20291.807| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 3.41 r_work: 0.3035 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10452 Z= 0.165 Angle : 0.602 9.407 14153 Z= 0.305 Chirality : 0.042 0.162 1599 Planarity : 0.004 0.062 1761 Dihedral : 6.169 98.013 1496 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.95 % Allowed : 13.88 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.26 (0.23), residues: 1272 helix: 1.42 (0.23), residues: 509 sheet: -1.04 (0.30), residues: 271 loop : -1.30 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.014 0.001 TYR E 190 PHE 0.011 0.001 PHE A 189 TRP 0.014 0.001 TRP A 131 HIS 0.006 0.001 HIS E 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (10450) covalent geometry : angle 0.60185 / 0.31 (14149) SS BOND : bond 0.00232 / 0.12 ( 2) SS BOND : angle 0.84212 / 0.46 ( 4) hydrogen bonds : bond 0.03468 / 2.31 ( 529) hydrogen bonds : angle 4.54000 / 3.27 ( 1530) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 171 time to evaluate : 0.352 Fit side-chains REVERT: R 26 MET cc_start: 0.6480 (OUTLIER) cc_final: 0.5509 (tpt) REVERT: R 56 TYR cc_start: 0.8175 (t80) cc_final: 0.7651 (t80) REVERT: R 65 ARG cc_start: 0.7510 (ttt180) cc_final: 0.6409 (mtm110) REVERT: R 207 TYR cc_start: 0.7832 (t80) cc_final: 0.7472 (t80) REVERT: R 240 ASP cc_start: 0.8480 (t0) cc_final: 0.8201 (t0) REVERT: R 276 GLN cc_start: 0.8845 (mm-40) cc_final: 0.8475 (pt0) REVERT: R 292 SER cc_start: 0.9047 (m) cc_final: 0.8723 (p) REVERT: R 305 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7893 (tm-30) REVERT: R 313 CYS cc_start: 0.7507 (OUTLIER) cc_final: 0.6972 (p) REVERT: A 51 LYS cc_start: 0.9275 (mttt) cc_final: 0.9001 (mmmt) REVERT: A 224 CYS cc_start: 0.8980 (m) cc_final: 0.8276 (p) REVERT: A 330 LYS cc_start: 0.8731 (mmtt) cc_final: 0.8258 (ptmt) REVERT: B 7 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8613 (mm) REVERT: B 10 GLU cc_start: 0.9539 (tp30) cc_final: 0.9327 (tp30) REVERT: B 101 MET cc_start: 0.9294 (mtp) cc_final: 0.8981 (mtp) REVERT: B 209 LYS cc_start: 0.8966 (mttm) cc_final: 0.8674 (mttt) REVERT: B 258 ASP cc_start: 0.8755 (t70) cc_final: 0.8468 (t0) REVERT: B 297 TRP cc_start: 0.9116 (m100) cc_final: 0.8134 (m100) REVERT: C 13 ARG cc_start: 0.9416 (mtt-85) cc_final: 0.8819 (ptp-110) REVERT: C 20 LYS cc_start: 0.9481 (ttpt) cc_final: 0.9092 (ptmm) REVERT: C 29 LYS cc_start: 0.8905 (mmmt) cc_final: 0.8691 (mmmt) REVERT: C 32 LYS cc_start: 0.9332 (tttt) cc_final: 0.9122 (tptp) REVERT: C 42 GLU cc_start: 0.9042 (tt0) cc_final: 0.8791 (tm-30) REVERT: C 58 GLU cc_start: 0.8785 (pt0) cc_final: 0.8177 (pm20) REVERT: E 73 ASP cc_start: 0.7995 (t70) cc_final: 0.6573 (t70) REVERT: E 93 MET cc_start: 0.8729 (ttm) cc_final: 0.8091 (tpt) REVERT: E 140 MET cc_start: 0.9192 (mmm) cc_final: 0.8479 (mmm) REVERT: E 220 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8553 (mm-30) REVERT: E 223 ASP cc_start: 0.8545 (m-30) cc_final: 0.7877 (m-30) outliers start: 43 outliers final: 24 residues processed: 203 average time/residue: 0.0894 time to fit residues: 26.1085 Evaluate side-chains 179 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 26 MET Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 267 HIS Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 312 HIS Chi-restraints excluded: chain R residue 313 CYS Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 69 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 9 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 93 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 40 optimal weight: 30.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.122596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.077841 restraints weight = 20229.628| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.30 r_work: 0.2934 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 10452 Z= 0.259 Angle : 0.657 7.751 14153 Z= 0.336 Chirality : 0.044 0.170 1599 Planarity : 0.004 0.061 1761 Dihedral : 6.510 101.100 1496 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.23 % Allowed : 14.71 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.23), residues: 1272 helix: 1.48 (0.23), residues: 514 sheet: -0.95 (0.29), residues: 279 loop : -1.03 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 304 TYR 0.021 0.002 TYR B 289 PHE 0.017 0.002 PHE B 151 TRP 0.013 0.002 TRP B 99 HIS 0.009 0.001 HIS E 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.26 (10450) covalent geometry : angle 0.65713 / 0.34 (14149) SS BOND : bond 0.00125 / 0.06 ( 2) SS BOND : angle 0.49315 / 0.26 ( 4) hydrogen bonds : bond 0.03674 / 2.48 ( 529) hydrogen bonds : angle 4.62529 / 3.29 ( 1530) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 158 time to evaluate : 0.371 Fit side-chains REVERT: R 26 MET cc_start: 0.6763 (OUTLIER) cc_final: 0.5844 (tpt) REVERT: R 49 LEU cc_start: 0.8808 (mt) cc_final: 0.8506 (tp) REVERT: R 56 TYR cc_start: 0.8379 (t80) cc_final: 0.7682 (t80) REVERT: R 65 ARG cc_start: 0.7678 (ttt180) cc_final: 0.6578 (mtm110) REVERT: R 70 TYR cc_start: 0.8812 (m-80) cc_final: 0.8571 (m-80) REVERT: R 207 TYR cc_start: 0.7975 (t80) cc_final: 0.7465 (t80) REVERT: R 289 LEU cc_start: 0.8766 (tp) cc_final: 0.8432 (tp) REVERT: R 292 SER cc_start: 0.9200 (m) cc_final: 0.8840 (p) REVERT: R 305 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7703 (tm-30) REVERT: R 313 CYS cc_start: 0.7521 (OUTLIER) cc_final: 0.6804 (p) REVERT: A 51 LYS cc_start: 0.9259 (mttt) cc_final: 0.9006 (mmmt) REVERT: A 330 LYS cc_start: 0.8805 (mmtt) cc_final: 0.8398 (ptmt) REVERT: B 7 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8622 (mm) REVERT: B 101 MET cc_start: 0.9284 (mtp) cc_final: 0.9006 (mtp) REVERT: B 209 LYS cc_start: 0.9051 (mttm) cc_final: 0.8721 (mttt) REVERT: B 258 ASP cc_start: 0.8716 (t70) cc_final: 0.8397 (t0) REVERT: C 20 LYS cc_start: 0.9477 (ttpt) cc_final: 0.9074 (ptmm) REVERT: C 29 LYS cc_start: 0.9025 (mmmt) cc_final: 0.8641 (mmmt) REVERT: C 58 GLU cc_start: 0.8791 (pt0) cc_final: 0.8126 (pm20) REVERT: E 73 ASP cc_start: 0.7851 (t70) cc_final: 0.7213 (t70) REVERT: E 82 GLN cc_start: 0.8256 (tp-100) cc_final: 0.7936 (tp-100) REVERT: E 93 MET cc_start: 0.8773 (ttm) cc_final: 0.8058 (tpt) REVERT: E 223 ASP cc_start: 0.8726 (m-30) cc_final: 0.7964 (m-30) outliers start: 46 outliers final: 32 residues processed: 191 average time/residue: 0.0891 time to fit residues: 24.4403 Evaluate side-chains 184 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 26 MET Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 267 HIS Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 312 HIS Chi-restraints excluded: chain R residue 313 CYS Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 4 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 52 optimal weight: 0.0020 chunk 119 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 276 GLN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.125164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.081367 restraints weight = 20054.824| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 3.30 r_work: 0.3004 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10452 Z= 0.142 Angle : 0.584 7.769 14153 Z= 0.297 Chirality : 0.041 0.171 1599 Planarity : 0.004 0.050 1761 Dihedral : 6.196 97.846 1496 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.40 % Allowed : 15.81 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.24), residues: 1272 helix: 1.74 (0.23), residues: 508 sheet: -0.75 (0.30), residues: 262 loop : -1.01 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 13 TYR 0.014 0.001 TYR E 190 PHE 0.012 0.001 PHE A 189 TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS E 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (10450) covalent geometry : angle 0.58420 / 0.30 (14149) SS BOND : bond 0.00145 / 0.07 ( 2) SS BOND : angle 0.45755 / 0.24 ( 4) hydrogen bonds : bond 0.03307 / 2.20 ( 529) hydrogen bonds : angle 4.42091 / 3.17 ( 1530) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: R 26 MET cc_start: 0.6655 (OUTLIER) cc_final: 0.5737 (tpt) REVERT: R 49 LEU cc_start: 0.8790 (mt) cc_final: 0.8527 (tp) REVERT: R 56 TYR cc_start: 0.8356 (t80) cc_final: 0.7868 (t80) REVERT: R 65 ARG cc_start: 0.7643 (ttt180) cc_final: 0.6588 (mtm110) REVERT: R 70 TYR cc_start: 0.8738 (m-80) cc_final: 0.8497 (m-80) REVERT: R 207 TYR cc_start: 0.7948 (t80) cc_final: 0.7376 (t80) REVERT: R 276 GLN cc_start: 0.8600 (mm-40) cc_final: 0.8069 (pt0) REVERT: R 292 SER cc_start: 0.9210 (m) cc_final: 0.8878 (p) REVERT: R 305 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7767 (tm-30) REVERT: R 313 CYS cc_start: 0.7477 (t) cc_final: 0.6944 (p) REVERT: A 51 LYS cc_start: 0.9281 (mttt) cc_final: 0.9027 (mmmt) REVERT: A 224 CYS cc_start: 0.8824 (m) cc_final: 0.8240 (p) REVERT: A 330 LYS cc_start: 0.8771 (mmtt) cc_final: 0.8383 (ptmt) REVERT: B 101 MET cc_start: 0.9210 (mtp) cc_final: 0.8952 (mtp) REVERT: B 209 LYS cc_start: 0.8937 (mttm) cc_final: 0.8625 (mttt) REVERT: B 258 ASP cc_start: 0.8631 (t70) cc_final: 0.8369 (t0) REVERT: B 262 MET cc_start: 0.8837 (mmm) cc_final: 0.8541 (mmp) REVERT: B 297 TRP cc_start: 0.9159 (m100) cc_final: 0.8348 (m100) REVERT: C 20 LYS cc_start: 0.9476 (ttpt) cc_final: 0.9068 (ptmm) REVERT: C 29 LYS cc_start: 0.8969 (mmmt) cc_final: 0.8710 (mmmt) REVERT: C 58 GLU cc_start: 0.8784 (pt0) cc_final: 0.8173 (pm20) REVERT: E 73 ASP cc_start: 0.7809 (t70) cc_final: 0.7162 (t0) REVERT: E 82 GLN cc_start: 0.8160 (tp-100) cc_final: 0.7889 (tp-100) REVERT: E 93 MET cc_start: 0.8716 (ttm) cc_final: 0.8125 (tpt) REVERT: E 220 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8196 (mm-30) REVERT: E 223 ASP cc_start: 0.8532 (m-30) cc_final: 0.8139 (m-30) outliers start: 37 outliers final: 23 residues processed: 191 average time/residue: 0.0929 time to fit residues: 25.6304 Evaluate side-chains 180 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 26 MET Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 312 HIS Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 90 optimal weight: 0.0970 chunk 109 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 218 GLN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.126786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.083423 restraints weight = 20371.669| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.31 r_work: 0.3050 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10452 Z= 0.112 Angle : 0.563 8.513 14153 Z= 0.284 Chirality : 0.040 0.225 1599 Planarity : 0.004 0.042 1761 Dihedral : 5.964 97.185 1496 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.94 % Allowed : 17.19 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.24), residues: 1272 helix: 1.89 (0.23), residues: 509 sheet: -0.67 (0.31), residues: 259 loop : -0.98 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 242 TYR 0.013 0.001 TYR E 190 PHE 0.009 0.001 PHE E 177 TRP 0.014 0.001 TRP B 211 HIS 0.003 0.001 HIS E 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (10450) covalent geometry : angle 0.56322 / 0.28 (14149) SS BOND : bond 0.00199 / 0.10 ( 2) SS BOND : angle 0.48967 / 0.25 ( 4) hydrogen bonds : bond 0.03159 / 2.10 ( 529) hydrogen bonds : angle 4.31149 / 3.10 ( 1530) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: R 26 MET cc_start: 0.6709 (OUTLIER) cc_final: 0.6082 (tpp) REVERT: R 49 LEU cc_start: 0.8777 (mt) cc_final: 0.8521 (tp) REVERT: R 56 TYR cc_start: 0.8285 (t80) cc_final: 0.7849 (t80) REVERT: R 65 ARG cc_start: 0.7692 (ttt180) cc_final: 0.6592 (mtm110) REVERT: R 70 TYR cc_start: 0.8630 (m-80) cc_final: 0.8259 (m-80) REVERT: R 207 TYR cc_start: 0.7876 (t80) cc_final: 0.7397 (t80) REVERT: R 239 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7339 (pp) REVERT: R 276 GLN cc_start: 0.8552 (mm-40) cc_final: 0.7943 (pt0) REVERT: R 292 SER cc_start: 0.9236 (m) cc_final: 0.8878 (p) REVERT: R 305 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8019 (tm-30) REVERT: R 313 CYS cc_start: 0.7448 (t) cc_final: 0.7060 (p) REVERT: A 51 LYS cc_start: 0.9288 (mttt) cc_final: 0.9017 (mmmt) REVERT: A 224 CYS cc_start: 0.8875 (m) cc_final: 0.8265 (p) REVERT: A 330 LYS cc_start: 0.8765 (mmtt) cc_final: 0.8380 (ptmt) REVERT: B 207 SER cc_start: 0.8835 (m) cc_final: 0.8303 (p) REVERT: B 209 LYS cc_start: 0.8821 (mttm) cc_final: 0.8486 (mttt) REVERT: B 217 MET cc_start: 0.8725 (ppp) cc_final: 0.8120 (ppp) REVERT: B 258 ASP cc_start: 0.8616 (t70) cc_final: 0.8367 (t0) REVERT: B 262 MET cc_start: 0.8761 (mmm) cc_final: 0.8533 (mmp) REVERT: B 297 TRP cc_start: 0.9078 (m100) cc_final: 0.8449 (m100) REVERT: C 20 LYS cc_start: 0.9476 (ttpt) cc_final: 0.9074 (ptmm) REVERT: C 58 GLU cc_start: 0.8802 (pt0) cc_final: 0.8199 (pm20) REVERT: E 73 ASP cc_start: 0.7868 (t70) cc_final: 0.7243 (t0) REVERT: E 83 MET cc_start: 0.8854 (mtm) cc_final: 0.8529 (mtm) REVERT: E 93 MET cc_start: 0.8652 (ttm) cc_final: 0.8140 (tpt) REVERT: E 220 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8283 (mm-30) REVERT: E 223 ASP cc_start: 0.8397 (m-30) cc_final: 0.7981 (m-30) outliers start: 32 outliers final: 22 residues processed: 195 average time/residue: 0.0953 time to fit residues: 26.6758 Evaluate side-chains 184 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 26 MET Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 312 HIS Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 52 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 43 optimal weight: 20.0000 chunk 111 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 125 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.122622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.078327 restraints weight = 20214.288| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.27 r_work: 0.2950 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10452 Z= 0.230 Angle : 0.634 8.282 14153 Z= 0.322 Chirality : 0.043 0.158 1599 Planarity : 0.004 0.046 1761 Dihedral : 6.242 98.920 1496 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.03 % Allowed : 17.56 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.31 (0.24), residues: 1272 helix: 1.85 (0.23), residues: 506 sheet: -0.71 (0.29), residues: 284 loop : -0.95 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 242 TYR 0.013 0.002 TYR B 289 PHE 0.018 0.002 PHE B 292 TRP 0.018 0.001 TRP B 339 HIS 0.004 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.23 (10450) covalent geometry : angle 0.63371 / 0.32 (14149) SS BOND : bond 0.00129 / 0.06 ( 2) SS BOND : angle 0.41799 / 0.21 ( 4) hydrogen bonds : bond 0.03433 / 2.30 ( 529) hydrogen bonds : angle 4.47199 / 3.20 ( 1530) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: R 26 MET cc_start: 0.6830 (OUTLIER) cc_final: 0.6276 (tpp) REVERT: R 49 LEU cc_start: 0.8831 (mt) cc_final: 0.8570 (tp) REVERT: R 56 TYR cc_start: 0.8373 (t80) cc_final: 0.7923 (t80) REVERT: R 65 ARG cc_start: 0.7733 (ttt180) cc_final: 0.6616 (mtm110) REVERT: R 207 TYR cc_start: 0.7982 (t80) cc_final: 0.7602 (t80) REVERT: R 276 GLN cc_start: 0.8611 (mm-40) cc_final: 0.7979 (pt0) REVERT: R 292 SER cc_start: 0.9369 (m) cc_final: 0.9003 (p) REVERT: R 305 GLU cc_start: 0.8404 (tm-30) cc_final: 0.7992 (tm-30) REVERT: R 313 CYS cc_start: 0.7497 (OUTLIER) cc_final: 0.6965 (p) REVERT: A 51 LYS cc_start: 0.9298 (mttt) cc_final: 0.9037 (mmmt) REVERT: A 224 CYS cc_start: 0.9127 (m) cc_final: 0.8344 (p) REVERT: A 330 LYS cc_start: 0.8861 (mmtt) cc_final: 0.8417 (ptmt) REVERT: B 7 LEU cc_start: 0.8951 (mm) cc_final: 0.8744 (mm) REVERT: B 59 TYR cc_start: 0.9220 (m-80) cc_final: 0.9011 (m-80) REVERT: B 207 SER cc_start: 0.8855 (m) cc_final: 0.8354 (p) REVERT: B 209 LYS cc_start: 0.8904 (mttm) cc_final: 0.8691 (mttp) REVERT: B 258 ASP cc_start: 0.8596 (t70) cc_final: 0.8360 (t0) REVERT: B 262 MET cc_start: 0.8879 (mmm) cc_final: 0.8649 (mmp) REVERT: C 20 LYS cc_start: 0.9462 (ttpt) cc_final: 0.8993 (ptmm) REVERT: C 58 GLU cc_start: 0.8856 (pt0) cc_final: 0.8183 (pm20) REVERT: E 51 ILE cc_start: 0.8056 (mp) cc_final: 0.7565 (tt) REVERT: E 73 ASP cc_start: 0.7958 (t70) cc_final: 0.7408 (t70) REVERT: E 93 MET cc_start: 0.8790 (ttm) cc_final: 0.8070 (tpt) REVERT: E 153 GLU cc_start: 0.8607 (pm20) cc_final: 0.8405 (pm20) REVERT: E 220 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8360 (mm-30) REVERT: E 223 ASP cc_start: 0.8585 (m-30) cc_final: 0.8053 (m-30) outliers start: 33 outliers final: 24 residues processed: 184 average time/residue: 0.0921 time to fit residues: 24.6802 Evaluate side-chains 180 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 26 MET Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 312 HIS Chi-restraints excluded: chain R residue 313 CYS Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 83 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 43 optimal weight: 40.0000 chunk 76 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 90 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 54 optimal weight: 0.1980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.125362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.081800 restraints weight = 20074.570| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.27 r_work: 0.3018 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10452 Z= 0.126 Angle : 0.579 7.841 14153 Z= 0.293 Chirality : 0.040 0.161 1599 Planarity : 0.003 0.042 1761 Dihedral : 5.920 96.649 1496 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.67 % Allowed : 17.65 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.40 (0.24), residues: 1272 helix: 1.94 (0.23), residues: 509 sheet: -0.56 (0.29), residues: 286 loop : -1.01 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 13 TYR 0.013 0.001 TYR E 190 PHE 0.010 0.001 PHE A 189 TRP 0.013 0.001 TRP B 339 HIS 0.003 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (10450) covalent geometry : angle 0.57865 / 0.29 (14149) SS BOND : bond 0.00215 / 0.10 ( 2) SS BOND : angle 0.50061 / 0.26 ( 4) hydrogen bonds : bond 0.03166 / 2.10 ( 529) hydrogen bonds : angle 4.32074 / 3.12 ( 1530) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: R 26 MET cc_start: 0.6890 (mmm) cc_final: 0.6282 (tpp) REVERT: R 49 LEU cc_start: 0.8841 (mt) cc_final: 0.8587 (tp) REVERT: R 65 ARG cc_start: 0.7704 (ttt180) cc_final: 0.6551 (mtm110) REVERT: R 207 TYR cc_start: 0.7917 (t80) cc_final: 0.7350 (t80) REVERT: R 292 SER cc_start: 0.9304 (m) cc_final: 0.8957 (p) REVERT: R 305 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7996 (tm-30) REVERT: R 313 CYS cc_start: 0.7490 (OUTLIER) cc_final: 0.7048 (p) REVERT: A 51 LYS cc_start: 0.9271 (mttt) cc_final: 0.9021 (mmmt) REVERT: A 193 ASP cc_start: 0.7861 (t0) cc_final: 0.7322 (t0) REVERT: A 224 CYS cc_start: 0.9027 (m) cc_final: 0.8322 (p) REVERT: A 330 LYS cc_start: 0.8817 (mmtt) cc_final: 0.8390 (ptmt) REVERT: B 7 LEU cc_start: 0.8947 (mm) cc_final: 0.8715 (mm) REVERT: B 59 TYR cc_start: 0.9079 (m-80) cc_final: 0.8876 (m-80) REVERT: B 207 SER cc_start: 0.8944 (m) cc_final: 0.8439 (p) REVERT: B 209 LYS cc_start: 0.8820 (mttm) cc_final: 0.8546 (mttt) REVERT: B 258 ASP cc_start: 0.8608 (t70) cc_final: 0.8403 (t0) REVERT: B 297 TRP cc_start: 0.9141 (m100) cc_final: 0.8481 (m100) REVERT: B 339 TRP cc_start: 0.9042 (m100) cc_final: 0.8553 (m100) REVERT: C 20 LYS cc_start: 0.9453 (ttpt) cc_final: 0.8991 (ptmm) REVERT: C 58 GLU cc_start: 0.8805 (pt0) cc_final: 0.8203 (pm20) REVERT: E 34 MET cc_start: 0.9030 (mtp) cc_final: 0.8771 (mtp) REVERT: E 51 ILE cc_start: 0.7842 (mp) cc_final: 0.7466 (tt) REVERT: E 73 ASP cc_start: 0.7883 (t70) cc_final: 0.6917 (t0) REVERT: E 76 LYS cc_start: 0.9034 (mtmm) cc_final: 0.8627 (mtmm) REVERT: E 93 MET cc_start: 0.8650 (ttm) cc_final: 0.8083 (tpt) REVERT: E 220 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8388 (mm-30) REVERT: E 223 ASP cc_start: 0.8552 (m-30) cc_final: 0.8045 (m-30) outliers start: 29 outliers final: 24 residues processed: 187 average time/residue: 0.0941 time to fit residues: 25.1033 Evaluate side-chains 182 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 312 HIS Chi-restraints excluded: chain R residue 313 CYS Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 67 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.120753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.076378 restraints weight = 20221.532| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.22 r_work: 0.2907 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.5612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 10452 Z= 0.292 Angle : 0.686 7.264 14153 Z= 0.350 Chirality : 0.044 0.182 1599 Planarity : 0.004 0.041 1761 Dihedral : 6.339 98.666 1496 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.40 % Allowed : 17.37 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.25 (0.24), residues: 1272 helix: 1.77 (0.22), residues: 512 sheet: -0.75 (0.30), residues: 273 loop : -0.97 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 304 TYR 0.017 0.002 TYR B 289 PHE 0.020 0.002 PHE B 292 TRP 0.025 0.002 TRP B 339 HIS 0.006 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00662 / 0.29 (10450) covalent geometry : angle 0.68641 / 0.35 (14149) SS BOND : bond 0.00126 / 0.06 ( 2) SS BOND : angle 0.31753 / 0.15 ( 4) hydrogen bonds : bond 0.03632 / 2.44 ( 529) hydrogen bonds : angle 4.61562 / 3.30 ( 1530) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: R 26 MET cc_start: 0.7075 (OUTLIER) cc_final: 0.6098 (tpt) REVERT: R 49 LEU cc_start: 0.8926 (mt) cc_final: 0.8648 (tp) REVERT: R 65 ARG cc_start: 0.7842 (ttt180) cc_final: 0.6800 (mtm110) REVERT: R 207 TYR cc_start: 0.8073 (t80) cc_final: 0.7723 (t80) REVERT: R 292 SER cc_start: 0.9388 (m) cc_final: 0.8976 (p) REVERT: R 305 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7991 (tm-30) REVERT: R 313 CYS cc_start: 0.7501 (OUTLIER) cc_final: 0.6819 (p) REVERT: A 51 LYS cc_start: 0.9293 (mttt) cc_final: 0.9028 (mmmt) REVERT: A 330 LYS cc_start: 0.8947 (mmtt) cc_final: 0.8462 (ptmt) REVERT: B 7 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8699 (mm) REVERT: B 207 SER cc_start: 0.8958 (m) cc_final: 0.8443 (p) REVERT: B 209 LYS cc_start: 0.8981 (mttm) cc_final: 0.8739 (mttp) REVERT: B 258 ASP cc_start: 0.8636 (t70) cc_final: 0.8391 (t0) REVERT: C 20 LYS cc_start: 0.9462 (ttpt) cc_final: 0.9136 (mtpp) REVERT: C 58 GLU cc_start: 0.8900 (pt0) cc_final: 0.8234 (pm20) REVERT: E 34 MET cc_start: 0.9008 (mtp) cc_final: 0.8663 (mtp) REVERT: E 73 ASP cc_start: 0.8025 (t70) cc_final: 0.6955 (t70) REVERT: E 76 LYS cc_start: 0.9102 (mtmm) cc_final: 0.8630 (mtmm) REVERT: E 93 MET cc_start: 0.8872 (ttm) cc_final: 0.8086 (tpt) REVERT: E 153 GLU cc_start: 0.8657 (pm20) cc_final: 0.8405 (pm20) REVERT: E 220 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8284 (mm-30) REVERT: E 223 ASP cc_start: 0.8617 (m-30) cc_final: 0.8094 (m-30) outliers start: 37 outliers final: 27 residues processed: 177 average time/residue: 0.0981 time to fit residues: 24.9787 Evaluate side-chains 177 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 26 MET Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 312 HIS Chi-restraints excluded: chain R residue 313 CYS Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 1 optimal weight: 0.5980 chunk 101 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 25 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.122450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.078379 restraints weight = 20033.895| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.25 r_work: 0.2947 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.5652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10452 Z= 0.191 Angle : 0.641 10.386 14153 Z= 0.323 Chirality : 0.042 0.163 1599 Planarity : 0.004 0.042 1761 Dihedral : 6.091 96.504 1496 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.57 % Allowed : 18.47 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.32 (0.24), residues: 1272 helix: 1.83 (0.22), residues: 512 sheet: -0.60 (0.31), residues: 265 loop : -1.02 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 13 TYR 0.016 0.002 TYR R 70 PHE 0.013 0.001 PHE B 292 TRP 0.013 0.001 TRP E 36 HIS 0.004 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (10450) covalent geometry : angle 0.64094 / 0.32 (14149) SS BOND : bond 0.00227 / 0.11 ( 2) SS BOND : angle 0.37569 / 0.19 ( 4) hydrogen bonds : bond 0.03385 / 2.25 ( 529) hydrogen bonds : angle 4.48211 / 3.21 ( 1530) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 26 MET cc_start: 0.7077 (mmm) cc_final: 0.6232 (tpt) REVERT: R 49 LEU cc_start: 0.8896 (mt) cc_final: 0.8642 (tp) REVERT: R 65 ARG cc_start: 0.7812 (ttt180) cc_final: 0.6763 (mtm110) REVERT: R 207 TYR cc_start: 0.8000 (t80) cc_final: 0.7607 (t80) REVERT: R 292 SER cc_start: 0.9393 (m) cc_final: 0.9035 (p) REVERT: R 305 GLU cc_start: 0.8366 (tm-30) cc_final: 0.7998 (tm-30) REVERT: R 313 CYS cc_start: 0.7469 (OUTLIER) cc_final: 0.6882 (p) REVERT: A 51 LYS cc_start: 0.9244 (mttt) cc_final: 0.9015 (mmmt) REVERT: A 330 LYS cc_start: 0.8884 (mmtt) cc_final: 0.8445 (ptmt) REVERT: B 7 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8693 (mm) REVERT: B 101 MET cc_start: 0.9062 (mtp) cc_final: 0.8855 (mtp) REVERT: B 207 SER cc_start: 0.8936 (m) cc_final: 0.8444 (p) REVERT: B 209 LYS cc_start: 0.8918 (mttm) cc_final: 0.8701 (mttp) REVERT: B 258 ASP cc_start: 0.8588 (t70) cc_final: 0.8361 (t0) REVERT: C 13 ARG cc_start: 0.9311 (ttm110) cc_final: 0.9034 (ttm-80) REVERT: C 20 LYS cc_start: 0.9442 (ttpt) cc_final: 0.9106 (mtpp) REVERT: C 58 GLU cc_start: 0.8909 (pt0) cc_final: 0.8263 (pm20) REVERT: E 34 MET cc_start: 0.8972 (mtp) cc_final: 0.8634 (mtp) REVERT: E 73 ASP cc_start: 0.8013 (t70) cc_final: 0.6949 (t70) REVERT: E 76 LYS cc_start: 0.9103 (mtmm) cc_final: 0.8699 (mtmm) REVERT: E 93 MET cc_start: 0.8730 (ttm) cc_final: 0.8058 (tpt) REVERT: E 153 GLU cc_start: 0.8615 (pm20) cc_final: 0.8386 (pm20) REVERT: E 220 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8367 (mm-30) REVERT: E 223 ASP cc_start: 0.8612 (m-30) cc_final: 0.8098 (m-30) outliers start: 28 outliers final: 23 residues processed: 171 average time/residue: 0.1010 time to fit residues: 24.4564 Evaluate side-chains 176 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 312 HIS Chi-restraints excluded: chain R residue 313 CYS Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 101 optimal weight: 7.9990 chunk 90 optimal weight: 0.2980 chunk 41 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 42 optimal weight: 9.9990 chunk 87 optimal weight: 0.4980 chunk 106 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.124144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.080255 restraints weight = 20264.620| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.29 r_work: 0.2986 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.5620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10452 Z= 0.144 Angle : 0.623 11.656 14153 Z= 0.311 Chirality : 0.041 0.151 1599 Planarity : 0.004 0.042 1761 Dihedral : 5.867 95.170 1496 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.67 % Allowed : 18.20 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.46 (0.24), residues: 1272 helix: 1.98 (0.22), residues: 508 sheet: -0.48 (0.31), residues: 269 loop : -1.00 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 13 TYR 0.016 0.001 TYR R 70 PHE 0.011 0.001 PHE A 189 TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (10450) covalent geometry : angle 0.62302 / 0.31 (14149) SS BOND : bond 0.00222 / 0.11 ( 2) SS BOND : angle 0.45666 / 0.24 ( 4) hydrogen bonds : bond 0.03282 / 2.18 ( 529) hydrogen bonds : angle 4.35201 / 3.12 ( 1530) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2804.81 seconds wall clock time: 48 minutes 52.71 seconds (2932.71 seconds total)