Starting phenix.real_space_refine on Wed Mar 4 03:22:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pt0_20470/03_2026/6pt0_20470.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pt0_20470/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6pt0_20470/03_2026/6pt0_20470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pt0_20470/03_2026/6pt0_20470.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pt0_20470/03_2026/6pt0_20470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pt0_20470/03_2026/6pt0_20470.map" } 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-dev-5986/lib/python3.9/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: 2.60, per 1000 atoms: 0.25 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: 0.78 Conformation dependent library (CDL) restraints added in 469.8 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: 0.32 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: 1.41 Time building geometry restraints manager: 1.07 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: 6185 18.03 - 36.05: 193 36.05 - 54.08: 40 54.08 - 72.10: 4 72.10 - 90.13: 7 Dihedral angle restraints: 6429 sinusoidal: 2704 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 6426 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: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.870 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 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 : 10.149 90.128 4023 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 covalent geometry : bond 0.00606 (10450) covalent geometry : angle 0.88833 (14149) SS BOND : bond 0.00695 ( 2) SS BOND : angle 11.21410 ( 4) hydrogen bonds : bond 0.10955 ( 529) hydrogen bonds : angle 6.16697 ( 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 : 0.357 Fit side-chains 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: 0.7164 (t80) REVERT: R 65 ARG cc_start: 0.7497 (ttt180) cc_final: 0.6427 (mtm110) REVERT: R 66 ARG cc_start: 0.8744 (ttp-110) cc_final: 0.8449 (mtp85) 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: 0.7426 (p) REVERT: A 25 GLU cc_start: 0.8201 (tt0) cc_final: 0.7975 (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: 0.7474 (p) REVERT: A 330 LYS cc_start: 0.8346 (mmtt) cc_final: 0.7991 (pttm) REVERT: A 333 GLN cc_start: 0.8506 (tp40) cc_final: 0.7972 (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: 0.8475 (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: 0.8281 (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: 0.8428 (tp30) REVERT: E 52 SER cc_start: 0.8625 (m) cc_final: 0.8050 (t) REVERT: E 73 ASP cc_start: 0.7224 (t70) cc_final: 0.6291 (t70) REVERT: E 80 PHE cc_start: 0.7823 (m-80) cc_final: 0.7426 (m-80) REVERT: E 223 ASP cc_start: 0.8605 (m-30) cc_final: 0.7125 (m-30) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.1180 time to fit residues: 55.9069 Evaluate side-chains 192 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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: 4.9990 chunk 123 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.126356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.082175 restraints weight = 20020.000| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.34 r_work: 0.3031 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 10452 Z= 0.258 Angle : 0.708 9.505 14153 Z= 0.361 Chirality : 0.045 0.180 1599 Planarity : 0.005 0.050 1761 Dihedral : 6.751 54.634 1728 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.31 % Allowed : 12.59 % Favored : 84.10 % 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: -0.82 (0.22), residues: 1272 helix: 0.81 (0.22), residues: 510 sheet: -1.37 (0.30), residues: 271 loop : -1.42 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 96 TYR 0.018 0.002 TYR E 190 PHE 0.020 0.002 PHE B 151 TRP 0.022 0.002 TRP B 211 HIS 0.013 0.002 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00593 (10450) covalent geometry : angle 0.70777 (14149) SS BOND : bond 0.00373 ( 2) SS BOND : angle 1.12998 ( 4) hydrogen bonds : bond 0.03814 ( 529) hydrogen bonds : angle 4.85892 ( 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 220 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 0.446 Fit side-chains REVERT: R 26 MET cc_start: 0.6542 (OUTLIER) cc_final: 0.6075 (tpp) REVERT: R 56 TYR cc_start: 0.8077 (t80) cc_final: 0.7551 (t80) REVERT: R 65 ARG cc_start: 0.7496 (ttt180) cc_final: 0.6385 (mtm110) REVERT: R 130 ASP cc_start: 0.8940 (t70) cc_final: 0.8681 (t0) REVERT: R 207 TYR cc_start: 0.7864 (t80) cc_final: 0.7519 (t80) REVERT: R 276 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8636 (pt0) REVERT: R 283 PHE cc_start: 0.8059 (m-80) cc_final: 0.7738 (m-10) REVERT: R 292 SER cc_start: 0.8966 (m) cc_final: 0.8660 (p) REVERT: A 9 ASP cc_start: 0.9048 (m-30) cc_final: 0.8821 (m-30) REVERT: A 51 LYS cc_start: 0.9236 (mttt) cc_final: 0.8985 (mmmt) REVERT: A 198 MET cc_start: 0.8385 (mtp) cc_final: 0.8000 (ttp) REVERT: A 224 CYS cc_start: 0.8967 (m) cc_final: 0.8318 (p) REVERT: A 330 LYS cc_start: 0.8646 (mmtt) cc_final: 0.8252 (ptmt) REVERT: B 10 GLU cc_start: 0.9524 (tp30) cc_final: 0.9301 (tp30) REVERT: B 101 MET cc_start: 0.9335 (mtp) cc_final: 0.9011 (mtp) REVERT: B 209 LYS cc_start: 0.9128 (mttm) cc_final: 0.8830 (mttt) REVERT: B 243 THR cc_start: 0.9332 (m) cc_final: 0.8971 (p) REVERT: B 247 ASP cc_start: 0.8170 (t0) cc_final: 0.7745 (t0) REVERT: B 297 TRP cc_start: 0.9065 (m100) cc_final: 0.8153 (m100) REVERT: C 13 ARG cc_start: 0.9402 (mtt-85) cc_final: 0.8917 (ptp-110) REVERT: C 20 LYS cc_start: 0.9499 (ttpt) cc_final: 0.9112 (ptmm) REVERT: C 29 LYS cc_start: 0.8928 (mmmt) cc_final: 0.8585 (mmmt) REVERT: C 42 GLU cc_start: 0.8957 (tt0) cc_final: 0.8739 (tm-30) REVERT: C 58 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.7954 (pm20) REVERT: E 73 ASP cc_start: 0.7808 (t70) cc_final: 0.6146 (t70) REVERT: E 76 LYS cc_start: 0.9234 (mtmt) cc_final: 0.8797 (mtmm) REVERT: E 93 MET cc_start: 0.8781 (ttm) cc_final: 0.8084 (tpt) REVERT: E 140 MET cc_start: 0.9147 (mmm) cc_final: 0.8141 (mmm) REVERT: E 148 PRO cc_start: 0.9082 (Cg_endo) cc_final: 0.8841 (Cg_exo) REVERT: E 210 THR cc_start: 0.8373 (m) cc_final: 0.8160 (p) REVERT: E 220 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8261 (mp0) REVERT: E 223 ASP cc_start: 0.8463 (m-30) cc_final: 0.7211 (m-30) outliers start: 36 outliers final: 18 residues processed: 211 average time/residue: 0.0984 time to fit residues: 29.3625 Evaluate side-chains 176 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 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 C residue 58 GLU 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: 1.9990 chunk 37 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 57 optimal weight: 0.0000 chunk 116 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 259 GLN ** E 82 GLN ** 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 = 0.3941 r_free = 0.3941 target = 0.127453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.083887 restraints weight = 20217.252| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.38 r_work: 0.3049 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10452 Z= 0.144 Angle : 0.591 9.943 14153 Z= 0.301 Chirality : 0.042 0.154 1599 Planarity : 0.004 0.065 1761 Dihedral : 6.184 54.778 1728 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.58 % Allowed : 13.60 % Favored : 82.81 % 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: 1.40 (0.23), residues: 509 sheet: -1.07 (0.30), residues: 280 loop : -1.26 (0.27), residues: 483 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 0.011 0.001 TRP B 211 HIS 0.006 0.001 HIS E 232 Details of bonding type rmsd covalent geometry : bond 0.00324 (10450) covalent geometry : angle 0.59083 (14149) SS BOND : bond 0.00229 ( 2) SS BOND : angle 0.82436 ( 4) hydrogen bonds : bond 0.03442 ( 529) hydrogen bonds : angle 4.53817 ( 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 209 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 170 time to evaluate : 0.384 Fit side-chains REVERT: R 26 MET cc_start: 0.6491 (OUTLIER) cc_final: 0.5500 (tpt) REVERT: R 56 TYR cc_start: 0.8147 (t80) cc_final: 0.7650 (t80) REVERT: R 65 ARG cc_start: 0.7461 (ttt180) cc_final: 0.6376 (mtm110) REVERT: R 207 TYR cc_start: 0.7848 (t80) cc_final: 0.7473 (t80) REVERT: R 276 GLN cc_start: 0.8885 (mm-40) cc_final: 0.8496 (pt0) REVERT: R 283 PHE cc_start: 0.7946 (m-80) cc_final: 0.7700 (m-10) REVERT: R 292 SER cc_start: 0.8955 (m) cc_final: 0.8642 (p) REVERT: R 305 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7856 (tm-30) REVERT: R 313 CYS cc_start: 0.7511 (OUTLIER) cc_final: 0.6983 (p) REVERT: A 51 LYS cc_start: 0.9239 (mttt) cc_final: 0.8991 (mmmt) REVERT: A 224 CYS cc_start: 0.8985 (m) cc_final: 0.8304 (p) REVERT: A 330 LYS cc_start: 0.8712 (mmtt) cc_final: 0.8243 (ptmt) REVERT: B 7 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8617 (mm) REVERT: B 10 GLU cc_start: 0.9537 (tp30) cc_final: 0.9302 (tp30) REVERT: B 101 MET cc_start: 0.9271 (mtp) cc_final: 0.8958 (mtp) REVERT: B 209 LYS cc_start: 0.8958 (mttm) cc_final: 0.8530 (mttt) REVERT: B 211 TRP cc_start: 0.9189 (m100) cc_final: 0.8781 (m100) REVERT: B 258 ASP cc_start: 0.8766 (t70) cc_final: 0.8491 (t0) REVERT: B 297 TRP cc_start: 0.9106 (m100) cc_final: 0.8137 (m100) REVERT: C 13 ARG cc_start: 0.9417 (mtt-85) cc_final: 0.8830 (ptp-110) REVERT: C 20 LYS cc_start: 0.9483 (ttpt) cc_final: 0.9101 (ptmm) REVERT: C 42 GLU cc_start: 0.9018 (tt0) cc_final: 0.8780 (tm-30) REVERT: C 58 GLU cc_start: 0.8797 (pt0) cc_final: 0.8008 (pm20) REVERT: E 45 LEU cc_start: 0.9133 (mt) cc_final: 0.8921 (mt) REVERT: E 73 ASP cc_start: 0.7920 (t70) cc_final: 0.6256 (t70) REVERT: E 76 LYS cc_start: 0.9264 (mtmt) cc_final: 0.8815 (mtmm) REVERT: E 93 MET cc_start: 0.8712 (ttm) cc_final: 0.8072 (tpt) REVERT: E 140 MET cc_start: 0.9206 (mmm) cc_final: 0.8400 (mmm) REVERT: E 210 THR cc_start: 0.8447 (m) cc_final: 0.8206 (p) REVERT: E 220 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8498 (mm-30) REVERT: E 223 ASP cc_start: 0.8673 (m-30) cc_final: 0.7844 (m-30) outliers start: 39 outliers final: 24 residues processed: 200 average time/residue: 0.1028 time to fit residues: 29.2333 Evaluate side-chains 178 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 293 MET 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 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: 10.0000 chunk 55 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 93 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 40 optimal weight: 40.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS A 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.121729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.077026 restraints weight = 20286.530| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.30 r_work: 0.2926 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 10452 Z= 0.287 Angle : 0.681 7.867 14153 Z= 0.348 Chirality : 0.045 0.164 1599 Planarity : 0.005 0.062 1761 Dihedral : 6.654 57.226 1728 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.04 % Allowed : 14.25 % Favored : 81.71 % 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: -0.15 (0.23), residues: 1272 helix: 1.40 (0.23), residues: 512 sheet: -1.01 (0.29), residues: 278 loop : -1.11 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 229 TYR 0.023 0.002 TYR B 289 PHE 0.017 0.002 PHE B 151 TRP 0.013 0.002 TRP B 99 HIS 0.009 0.002 HIS E 232 Details of bonding type rmsd covalent geometry : bond 0.00652 (10450) covalent geometry : angle 0.68070 (14149) SS BOND : bond 0.00067 ( 2) SS BOND : angle 0.41981 ( 4) hydrogen bonds : bond 0.03752 ( 529) hydrogen bonds : angle 4.66117 ( 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 200 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 156 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: R 49 LEU cc_start: 0.8819 (mt) cc_final: 0.8519 (tp) REVERT: R 56 TYR cc_start: 0.8378 (t80) cc_final: 0.7707 (t80) REVERT: R 65 ARG cc_start: 0.7685 (ttt180) cc_final: 0.6575 (mtm110) REVERT: R 70 TYR cc_start: 0.8857 (m-80) cc_final: 0.8601 (m-80) REVERT: R 207 TYR cc_start: 0.8007 (t80) cc_final: 0.7653 (t80) REVERT: R 276 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8347 (pt0) REVERT: R 283 PHE cc_start: 0.8180 (m-80) cc_final: 0.7905 (m-10) REVERT: R 289 LEU cc_start: 0.8751 (tp) cc_final: 0.8382 (tp) REVERT: R 292 SER cc_start: 0.9188 (m) cc_final: 0.8844 (p) REVERT: R 305 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7647 (tm-30) REVERT: R 313 CYS cc_start: 0.7541 (OUTLIER) cc_final: 0.6834 (p) REVERT: A 51 LYS cc_start: 0.9271 (mttt) cc_final: 0.9024 (mmmt) REVERT: A 330 LYS cc_start: 0.8811 (mmtt) cc_final: 0.8403 (ptmt) REVERT: B 7 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8625 (mm) REVERT: B 101 MET cc_start: 0.9260 (mtp) cc_final: 0.8974 (mtp) REVERT: B 209 LYS cc_start: 0.9049 (mttm) cc_final: 0.8727 (mttt) REVERT: B 258 ASP cc_start: 0.8717 (t70) cc_final: 0.8400 (t0) REVERT: C 13 ARG cc_start: 0.9415 (mtt-85) cc_final: 0.8813 (ptp-110) REVERT: C 20 LYS cc_start: 0.9478 (ttpt) cc_final: 0.9064 (ptmm) REVERT: C 29 LYS cc_start: 0.8815 (mmmt) cc_final: 0.8547 (mmmt) REVERT: C 58 GLU cc_start: 0.8787 (pt0) cc_final: 0.8109 (pm20) REVERT: E 73 ASP cc_start: 0.8197 (t70) cc_final: 0.7432 (t0) REVERT: E 82 GLN cc_start: 0.8307 (tp-100) cc_final: 0.7951 (tp-100) REVERT: E 93 MET cc_start: 0.8791 (ttm) cc_final: 0.8067 (tpt) REVERT: E 223 ASP cc_start: 0.8539 (m-30) cc_final: 0.8195 (m-30) outliers start: 44 outliers final: 32 residues processed: 187 average time/residue: 0.0962 time to fit residues: 25.5715 Evaluate side-chains 182 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 51 ILE 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: 1.9990 chunk 89 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 98 HIS R 218 GLN ** A 244 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.124410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.080471 restraints weight = 19981.960| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.28 r_work: 0.2992 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10452 Z= 0.146 Angle : 0.584 7.258 14153 Z= 0.297 Chirality : 0.041 0.152 1599 Planarity : 0.004 0.053 1761 Dihedral : 6.320 56.427 1728 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.68 % Allowed : 15.53 % 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: 0.15 (0.24), residues: 1272 helix: 1.57 (0.23), residues: 515 sheet: -0.63 (0.30), residues: 272 loop : -1.02 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 242 TYR 0.014 0.001 TYR E 190 PHE 0.011 0.001 PHE A 189 TRP 0.013 0.001 TRP E 111 HIS 0.005 0.001 HIS E 232 Details of bonding type rmsd covalent geometry : bond 0.00332 (10450) covalent geometry : angle 0.58393 (14149) SS BOND : bond 0.00163 ( 2) SS BOND : angle 0.46635 ( 4) hydrogen bonds : bond 0.03335 ( 529) hydrogen bonds : angle 4.42243 ( 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 200 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: R 49 LEU cc_start: 0.8784 (mt) cc_final: 0.8520 (tp) REVERT: R 56 TYR cc_start: 0.8362 (t80) cc_final: 0.7869 (t80) REVERT: R 65 ARG cc_start: 0.7670 (ttt180) cc_final: 0.6595 (mtm110) REVERT: R 70 TYR cc_start: 0.8735 (m-80) cc_final: 0.8512 (m-80) REVERT: R 207 TYR cc_start: 0.7948 (t80) cc_final: 0.7393 (t80) REVERT: R 276 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8241 (pt0) REVERT: R 292 SER cc_start: 0.9159 (m) cc_final: 0.8830 (p) REVERT: R 305 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7675 (tm-30) REVERT: R 313 CYS cc_start: 0.7518 (t) cc_final: 0.6956 (p) REVERT: A 51 LYS cc_start: 0.9291 (mttt) cc_final: 0.9038 (mmmt) REVERT: A 224 CYS cc_start: 0.9067 (m) cc_final: 0.8325 (p) REVERT: A 330 LYS cc_start: 0.8781 (mmtt) cc_final: 0.8387 (ptmt) REVERT: B 7 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8642 (mm) REVERT: B 101 MET cc_start: 0.9201 (mtp) cc_final: 0.8944 (mtp) REVERT: B 209 LYS cc_start: 0.8934 (mttm) cc_final: 0.8623 (mttt) REVERT: B 258 ASP cc_start: 0.8665 (t70) cc_final: 0.8392 (t0) REVERT: B 262 MET cc_start: 0.8924 (mmm) cc_final: 0.8628 (mmp) REVERT: B 297 TRP cc_start: 0.9174 (m100) cc_final: 0.8264 (m100) REVERT: C 13 ARG cc_start: 0.9432 (mtt-85) cc_final: 0.8884 (ptp-110) REVERT: C 16 VAL cc_start: 0.9312 (t) cc_final: 0.9031 (m) REVERT: C 20 LYS cc_start: 0.9470 (ttpt) cc_final: 0.9072 (ptmm) REVERT: C 29 LYS cc_start: 0.8876 (mmmt) cc_final: 0.8585 (mmmt) REVERT: C 58 GLU cc_start: 0.8801 (pt0) cc_final: 0.8205 (pm20) REVERT: E 73 ASP cc_start: 0.8133 (t70) cc_final: 0.7459 (t0) REVERT: E 82 GLN cc_start: 0.8217 (tp-100) cc_final: 0.7885 (tp-100) REVERT: E 93 MET cc_start: 0.8721 (ttm) cc_final: 0.8124 (tpt) REVERT: E 153 GLU cc_start: 0.8643 (pm20) cc_final: 0.8402 (pm20) REVERT: E 220 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8198 (mm-30) REVERT: E 223 ASP cc_start: 0.8630 (m-30) cc_final: 0.8183 (m-30) outliers start: 40 outliers final: 25 residues processed: 189 average time/residue: 0.1003 time to fit residues: 27.0466 Evaluate side-chains 181 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 90 ARG Chi-restraints excluded: chain A residue 222 ILE 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 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: 0.9980 chunk 100 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 109 optimal weight: 0.0010 chunk 31 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3897 r_free = 0.3897 target = 0.124277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.080325 restraints weight = 20389.170| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 3.31 r_work: 0.2986 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10452 Z= 0.154 Angle : 0.584 7.464 14153 Z= 0.297 Chirality : 0.041 0.157 1599 Planarity : 0.004 0.047 1761 Dihedral : 6.334 57.480 1728 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.58 % Allowed : 16.08 % Favored : 80.33 % 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 (0.24), residues: 1272 helix: 1.76 (0.23), residues: 509 sheet: -0.58 (0.30), residues: 278 loop : -1.04 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 242 TYR 0.013 0.001 TYR E 190 PHE 0.012 0.001 PHE B 292 TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00353 (10450) covalent geometry : angle 0.58427 (14149) SS BOND : bond 0.00155 ( 2) SS BOND : angle 0.43734 ( 4) hydrogen bonds : bond 0.03304 ( 529) hydrogen bonds : angle 4.37353 ( 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 200 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: R 22 MET cc_start: 0.6763 (mmp) cc_final: 0.6512 (mmp) REVERT: R 26 MET cc_start: 0.6513 (tpp) cc_final: 0.6292 (tpp) REVERT: R 49 LEU cc_start: 0.8792 (mt) cc_final: 0.8526 (tp) REVERT: R 56 TYR cc_start: 0.8351 (t80) cc_final: 0.7875 (t80) REVERT: R 65 ARG cc_start: 0.7734 (ttt180) cc_final: 0.6585 (mtm110) REVERT: R 70 TYR cc_start: 0.8708 (m-80) cc_final: 0.8482 (m-80) REVERT: R 207 TYR cc_start: 0.7929 (t80) cc_final: 0.7367 (t80) REVERT: R 276 GLN cc_start: 0.8788 (mm-40) cc_final: 0.8241 (pt0) REVERT: R 289 LEU cc_start: 0.8689 (tp) cc_final: 0.8437 (tp) REVERT: R 292 SER cc_start: 0.9184 (m) cc_final: 0.8842 (p) REVERT: R 305 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7910 (tm-30) REVERT: R 313 CYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7040 (p) REVERT: A 51 LYS cc_start: 0.9278 (mttt) cc_final: 0.9026 (mmmt) REVERT: A 198 MET cc_start: 0.8262 (mtp) cc_final: 0.8032 (ttp) REVERT: A 224 CYS cc_start: 0.8797 (m) cc_final: 0.8270 (p) REVERT: A 229 ASP cc_start: 0.7500 (p0) cc_final: 0.7233 (t0) REVERT: A 330 LYS cc_start: 0.8785 (mmtt) cc_final: 0.8388 (ptmt) REVERT: B 101 MET cc_start: 0.9182 (mtp) cc_final: 0.8916 (mtp) REVERT: B 207 SER cc_start: 0.8843 (m) cc_final: 0.8281 (p) REVERT: B 209 LYS cc_start: 0.8904 (mttm) cc_final: 0.8622 (mttt) REVERT: B 262 MET cc_start: 0.8864 (mmm) cc_final: 0.8609 (mmp) REVERT: B 297 TRP cc_start: 0.9180 (m100) cc_final: 0.8347 (m100) REVERT: C 13 ARG cc_start: 0.9456 (mtt-85) cc_final: 0.8914 (ptp-110) REVERT: C 20 LYS cc_start: 0.9450 (ttpt) cc_final: 0.9159 (mtpp) REVERT: C 58 GLU cc_start: 0.8810 (pt0) cc_final: 0.8182 (pm20) REVERT: E 73 ASP cc_start: 0.8164 (t70) cc_final: 0.7473 (t0) REVERT: E 82 GLN cc_start: 0.8205 (tp-100) cc_final: 0.7888 (tp-100) REVERT: E 93 MET cc_start: 0.8696 (ttm) cc_final: 0.8057 (tpt) REVERT: E 153 GLU cc_start: 0.8547 (pm20) cc_final: 0.8327 (pm20) REVERT: E 220 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8265 (mm-30) REVERT: E 223 ASP cc_start: 0.8497 (m-30) cc_final: 0.7960 (m-30) outliers start: 39 outliers final: 29 residues processed: 189 average time/residue: 0.0963 time to fit residues: 26.2635 Evaluate side-chains 184 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 CYS 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 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 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 42 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 Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 43 optimal weight: 7.9990 chunk 111 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 chunk 2 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 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 = 0.3913 r_free = 0.3913 target = 0.125398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.081705 restraints weight = 20158.480| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 3.30 r_work: 0.3015 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10452 Z= 0.129 Angle : 0.581 8.331 14153 Z= 0.294 Chirality : 0.041 0.206 1599 Planarity : 0.004 0.046 1761 Dihedral : 6.219 58.223 1728 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.85 % Allowed : 16.82 % Favored : 80.33 % 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: 0.33 (0.24), residues: 1272 helix: 1.84 (0.23), residues: 508 sheet: -0.53 (0.29), residues: 286 loop : -1.03 (0.28), residues: 478 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 0.011 0.001 PHE A 189 TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00293 (10450) covalent geometry : angle 0.58140 (14149) SS BOND : bond 0.00192 ( 2) SS BOND : angle 0.50842 ( 4) hydrogen bonds : bond 0.03226 ( 529) hydrogen bonds : angle 4.31611 ( 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 198 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: R 22 MET cc_start: 0.6607 (mmp) cc_final: 0.6306 (mmt) REVERT: R 26 MET cc_start: 0.6608 (tpp) cc_final: 0.6325 (tpp) REVERT: R 49 LEU cc_start: 0.8788 (mt) cc_final: 0.8535 (tp) REVERT: R 56 TYR cc_start: 0.8296 (t80) cc_final: 0.7848 (t80) REVERT: R 65 ARG cc_start: 0.7639 (ttt180) cc_final: 0.6459 (mtm110) REVERT: R 70 TYR cc_start: 0.8659 (m-80) cc_final: 0.8350 (m-80) REVERT: R 207 TYR cc_start: 0.7940 (t80) cc_final: 0.7379 (t80) REVERT: R 276 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8258 (pt0) REVERT: R 292 SER cc_start: 0.9196 (m) cc_final: 0.8877 (p) REVERT: R 305 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8008 (tm-30) REVERT: R 313 CYS cc_start: 0.7513 (t) cc_final: 0.7130 (p) REVERT: A 51 LYS cc_start: 0.9281 (mttt) cc_final: 0.9033 (mmmt) REVERT: A 193 ASP cc_start: 0.7891 (t0) cc_final: 0.7354 (t0) REVERT: A 224 CYS cc_start: 0.8785 (m) cc_final: 0.8300 (p) REVERT: A 229 ASP cc_start: 0.7448 (p0) cc_final: 0.7209 (t0) REVERT: A 330 LYS cc_start: 0.8781 (mmtt) cc_final: 0.8383 (ptmt) REVERT: B 59 TYR cc_start: 0.9127 (m-80) cc_final: 0.8924 (m-80) REVERT: B 207 SER cc_start: 0.8832 (m) cc_final: 0.8366 (p) REVERT: B 209 LYS cc_start: 0.8858 (mttm) cc_final: 0.8603 (mttt) REVERT: B 297 TRP cc_start: 0.9144 (m100) cc_final: 0.8472 (m100) REVERT: C 13 ARG cc_start: 0.9452 (mtt-85) cc_final: 0.8906 (ptp-110) REVERT: C 20 LYS cc_start: 0.9441 (ttpt) cc_final: 0.9116 (mtpp) REVERT: C 58 GLU cc_start: 0.8815 (pt0) cc_final: 0.8206 (pm20) REVERT: E 73 ASP cc_start: 0.8155 (t70) cc_final: 0.7464 (t0) REVERT: E 93 MET cc_start: 0.8664 (ttm) cc_final: 0.8072 (tpt) REVERT: E 220 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8313 (mm-30) REVERT: E 223 ASP cc_start: 0.8501 (m-30) cc_final: 0.7990 (m-30) outliers start: 31 outliers final: 25 residues processed: 190 average time/residue: 0.1077 time to fit residues: 28.9809 Evaluate side-chains 181 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 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 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 C residue 42 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 69 THR 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: 0.7980 chunk 33 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 76 optimal weight: 0.2980 chunk 102 optimal weight: 0.7980 chunk 0 optimal weight: 40.0000 chunk 90 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 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 = 0.3925 r_free = 0.3925 target = 0.126254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.082975 restraints weight = 20017.883| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 3.28 r_work: 0.3042 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10452 Z= 0.118 Angle : 0.590 9.477 14153 Z= 0.295 Chirality : 0.040 0.169 1599 Planarity : 0.004 0.045 1761 Dihedral : 6.098 59.210 1728 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.85 % Allowed : 17.28 % 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: 0.43 (0.24), residues: 1272 helix: 1.93 (0.23), residues: 508 sheet: -0.47 (0.30), residues: 281 loop : -1.01 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 8 TYR 0.013 0.001 TYR E 190 PHE 0.011 0.001 PHE A 189 TRP 0.012 0.001 TRP B 211 HIS 0.003 0.000 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00266 (10450) covalent geometry : angle 0.58967 (14149) SS BOND : bond 0.00222 ( 2) SS BOND : angle 0.55057 ( 4) hydrogen bonds : bond 0.03137 ( 529) hydrogen bonds : angle 4.23439 ( 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 199 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: R 26 MET cc_start: 0.6745 (tpp) cc_final: 0.6461 (tpp) REVERT: R 49 LEU cc_start: 0.8792 (mt) cc_final: 0.8534 (tp) REVERT: R 56 TYR cc_start: 0.8254 (t80) cc_final: 0.7818 (t80) REVERT: R 65 ARG cc_start: 0.7612 (ttt180) cc_final: 0.6484 (mtm110) REVERT: R 70 TYR cc_start: 0.8621 (m-80) cc_final: 0.8223 (m-80) REVERT: R 207 TYR cc_start: 0.7914 (t80) cc_final: 0.7325 (t80) REVERT: R 276 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8214 (pt0) REVERT: R 292 SER cc_start: 0.9199 (m) cc_final: 0.8893 (p) REVERT: R 305 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8049 (tm-30) REVERT: R 313 CYS cc_start: 0.7460 (t) cc_final: 0.7096 (p) REVERT: A 51 LYS cc_start: 0.9209 (mttt) cc_final: 0.8987 (mmmt) REVERT: A 193 ASP cc_start: 0.7902 (t0) cc_final: 0.7341 (t0) REVERT: A 224 CYS cc_start: 0.8655 (m) cc_final: 0.8302 (p) REVERT: A 229 ASP cc_start: 0.7435 (p0) cc_final: 0.7208 (t0) REVERT: A 330 LYS cc_start: 0.8794 (mmtt) cc_final: 0.8392 (ptmt) REVERT: B 15 LYS cc_start: 0.9444 (mtmm) cc_final: 0.9168 (mttp) REVERT: B 59 TYR cc_start: 0.9081 (m-80) cc_final: 0.8824 (m-80) REVERT: B 207 SER cc_start: 0.8843 (m) cc_final: 0.8393 (p) REVERT: B 209 LYS cc_start: 0.8797 (mttm) cc_final: 0.8548 (mttt) REVERT: B 262 MET cc_start: 0.8510 (mmm) cc_final: 0.8274 (mmm) REVERT: B 289 TYR cc_start: 0.8786 (m-80) cc_final: 0.8529 (m-80) REVERT: B 297 TRP cc_start: 0.9083 (m100) cc_final: 0.8465 (m100) REVERT: C 13 ARG cc_start: 0.9466 (mtt-85) cc_final: 0.8880 (ptp-110) REVERT: C 20 LYS cc_start: 0.9446 (ttpt) cc_final: 0.9005 (ptmm) REVERT: C 58 GLU cc_start: 0.8826 (pt0) cc_final: 0.8257 (pm20) REVERT: E 73 ASP cc_start: 0.8148 (t70) cc_final: 0.6518 (t0) REVERT: E 76 LYS cc_start: 0.9237 (mtmt) cc_final: 0.8805 (mtmm) REVERT: E 93 MET cc_start: 0.8638 (ttm) cc_final: 0.8143 (tpt) REVERT: E 220 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8315 (mm-30) REVERT: E 223 ASP cc_start: 0.8478 (m-30) cc_final: 0.7979 (m-30) outliers start: 31 outliers final: 26 residues processed: 189 average time/residue: 0.1086 time to fit residues: 28.4902 Evaluate side-chains 183 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 A residue 90 ARG Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 316 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 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 42 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 69 THR 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: 6.9990 chunk 82 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 87 optimal weight: 0.0980 chunk 66 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3885 r_free = 0.3885 target = 0.123519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.079742 restraints weight = 20079.638| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.25 r_work: 0.2976 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10452 Z= 0.187 Angle : 0.633 9.325 14153 Z= 0.319 Chirality : 0.042 0.176 1599 Planarity : 0.004 0.045 1761 Dihedral : 6.315 60.908 1728 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.94 % Allowed : 17.83 % 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: 0.42 (0.24), residues: 1272 helix: 1.94 (0.23), residues: 508 sheet: -0.54 (0.29), residues: 288 loop : -0.98 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 242 TYR 0.014 0.002 TYR B 59 PHE 0.014 0.001 PHE B 292 TRP 0.023 0.001 TRP B 339 HIS 0.004 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00428 (10450) covalent geometry : angle 0.63335 (14149) SS BOND : bond 0.00172 ( 2) SS BOND : angle 0.42497 ( 4) hydrogen bonds : bond 0.03267 ( 529) hydrogen bonds : angle 4.33856 ( 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: 32 poor density : 158 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: R 26 MET cc_start: 0.6576 (tpp) cc_final: 0.6318 (tpp) REVERT: R 49 LEU cc_start: 0.8847 (mt) cc_final: 0.8592 (tp) REVERT: R 56 TYR cc_start: 0.8341 (t80) cc_final: 0.7909 (t80) REVERT: R 65 ARG cc_start: 0.7716 (ttt180) cc_final: 0.6546 (mtm110) REVERT: R 70 TYR cc_start: 0.8707 (m-80) cc_final: 0.8463 (m-80) REVERT: R 207 TYR cc_start: 0.7975 (t80) cc_final: 0.7391 (t80) REVERT: R 276 GLN cc_start: 0.8788 (mm-40) cc_final: 0.8516 (mm110) REVERT: R 292 SER cc_start: 0.9239 (m) cc_final: 0.8918 (p) REVERT: R 305 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8011 (tm-30) REVERT: R 313 CYS cc_start: 0.7454 (OUTLIER) cc_final: 0.7044 (p) REVERT: A 51 LYS cc_start: 0.9226 (mttt) cc_final: 0.8996 (mmmt) REVERT: A 193 ASP cc_start: 0.7879 (t0) cc_final: 0.7336 (t0) REVERT: A 224 CYS cc_start: 0.8813 (m) cc_final: 0.8299 (p) REVERT: A 330 LYS cc_start: 0.8837 (mmtt) cc_final: 0.8410 (ptmt) REVERT: B 207 SER cc_start: 0.8915 (m) cc_final: 0.8428 (p) REVERT: B 209 LYS cc_start: 0.8918 (mttm) cc_final: 0.8628 (mttt) REVERT: B 262 MET cc_start: 0.8575 (mmm) cc_final: 0.8274 (mmm) REVERT: C 13 ARG cc_start: 0.9483 (mtt-85) cc_final: 0.8901 (ptp-110) REVERT: C 20 LYS cc_start: 0.9464 (ttpt) cc_final: 0.9164 (mtpp) REVERT: C 58 GLU cc_start: 0.8799 (pt0) cc_final: 0.8146 (pm20) REVERT: E 73 ASP cc_start: 0.8186 (t70) cc_final: 0.6601 (t0) REVERT: E 76 LYS cc_start: 0.9282 (mtmt) cc_final: 0.8813 (mtmm) REVERT: E 93 MET cc_start: 0.8707 (ttm) cc_final: 0.8019 (tpt) REVERT: E 220 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8280 (mm-30) REVERT: E 223 ASP cc_start: 0.8497 (m-30) cc_final: 0.7984 (m-30) outliers start: 32 outliers final: 31 residues processed: 179 average time/residue: 0.1038 time to fit residues: 26.2374 Evaluate side-chains 187 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 135 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 267 HIS 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 A residue 247 MET Chi-restraints excluded: chain A residue 316 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 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 C residue 42 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 69 THR 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: 0.8980 chunk 101 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 25 optimal weight: 40.0000 chunk 47 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3894 r_free = 0.3894 target = 0.124198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.080380 restraints weight = 19898.699| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 3.25 r_work: 0.2993 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10452 Z= 0.161 Angle : 0.634 9.171 14153 Z= 0.318 Chirality : 0.042 0.166 1599 Planarity : 0.004 0.047 1761 Dihedral : 6.268 61.335 1728 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.31 % Allowed : 17.56 % 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: 1.94 (0.22), residues: 508 sheet: -0.51 (0.31), residues: 271 loop : -0.92 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 242 TYR 0.013 0.001 TYR E 190 PHE 0.012 0.001 PHE B 292 TRP 0.019 0.001 TRP B 339 HIS 0.003 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00369 (10450) covalent geometry : angle 0.63369 (14149) SS BOND : bond 0.00216 ( 2) SS BOND : angle 0.41997 ( 4) hydrogen bonds : bond 0.03206 ( 529) hydrogen bonds : angle 4.33323 ( 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 196 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: R 26 MET cc_start: 0.6753 (tpp) cc_final: 0.6479 (tpp) REVERT: R 49 LEU cc_start: 0.8823 (mt) cc_final: 0.8590 (tp) REVERT: R 56 TYR cc_start: 0.8327 (t80) cc_final: 0.7908 (t80) REVERT: R 65 ARG cc_start: 0.7754 (ttt180) cc_final: 0.6657 (mtm110) REVERT: R 70 TYR cc_start: 0.8683 (m-80) cc_final: 0.8394 (m-80) REVERT: R 207 TYR cc_start: 0.7954 (t80) cc_final: 0.7387 (t80) REVERT: R 276 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8532 (mm110) REVERT: R 292 SER cc_start: 0.9236 (m) cc_final: 0.8911 (p) REVERT: R 305 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8058 (tm-30) REVERT: R 313 CYS cc_start: 0.7424 (OUTLIER) cc_final: 0.7051 (p) REVERT: A 51 LYS cc_start: 0.9224 (mttt) cc_final: 0.8998 (mmmt) REVERT: A 193 ASP cc_start: 0.7867 (t0) cc_final: 0.7335 (t0) REVERT: A 224 CYS cc_start: 0.8722 (m) cc_final: 0.8277 (p) REVERT: A 330 LYS cc_start: 0.8830 (mmtt) cc_final: 0.8413 (ptmt) REVERT: B 207 SER cc_start: 0.8903 (m) cc_final: 0.8437 (p) REVERT: B 209 LYS cc_start: 0.8895 (mttm) cc_final: 0.8630 (mttt) REVERT: B 217 MET cc_start: 0.8710 (ppp) cc_final: 0.8160 (ppp) REVERT: B 297 TRP cc_start: 0.9191 (m100) cc_final: 0.8400 (m100) REVERT: C 13 ARG cc_start: 0.9475 (mtt-85) cc_final: 0.8903 (ptp-110) REVERT: C 20 LYS cc_start: 0.9485 (ttpt) cc_final: 0.9172 (mtpp) REVERT: C 58 GLU cc_start: 0.8850 (pt0) cc_final: 0.8098 (pm20) REVERT: E 34 MET cc_start: 0.8912 (mmm) cc_final: 0.8581 (mtp) REVERT: E 73 ASP cc_start: 0.8192 (t70) cc_final: 0.6604 (t0) REVERT: E 76 LYS cc_start: 0.9263 (mtmt) cc_final: 0.8813 (mtmm) REVERT: E 93 MET cc_start: 0.8682 (ttm) cc_final: 0.8024 (tpt) REVERT: E 220 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8295 (mm-30) REVERT: E 223 ASP cc_start: 0.8508 (m-30) cc_final: 0.8021 (m-30) outliers start: 36 outliers final: 33 residues processed: 183 average time/residue: 0.1058 time to fit residues: 27.3875 Evaluate side-chains 192 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 135 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 267 HIS 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 184 ILE Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 247 MET 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 C residue 42 GLU 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 69 THR 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: 1.9990 chunk 90 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.125429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.081889 restraints weight = 20140.097| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.28 r_work: 0.3020 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.5367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10452 Z= 0.134 Angle : 0.625 10.500 14153 Z= 0.313 Chirality : 0.041 0.159 1599 Planarity : 0.004 0.045 1761 Dihedral : 6.142 62.158 1728 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.22 % Allowed : 17.65 % 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: 0.53 (0.24), residues: 1272 helix: 2.01 (0.23), residues: 507 sheet: -0.48 (0.30), residues: 282 loop : -0.89 (0.29), residues: 483 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 0.011 0.001 PHE A 189 TRP 0.016 0.001 TRP B 339 HIS 0.003 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00306 (10450) covalent geometry : angle 0.62477 (14149) SS BOND : bond 0.00209 ( 2) SS BOND : angle 0.45299 ( 4) hydrogen bonds : bond 0.03159 ( 529) hydrogen bonds : angle 4.28590 ( 1530) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2895.62 seconds wall clock time: 50 minutes 24.66 seconds (3024.66 seconds total)