Starting phenix.real_space_refine on Mon Jul 28 14:54:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pt0_20470/07_2025/6pt0_20470.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pt0_20470/07_2025/6pt0_20470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pt0_20470/07_2025/6pt0_20470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pt0_20470/07_2025/6pt0_20470.map" model { file = "/net/cci-nas-00/data/ceres_data/6pt0_20470/07_2025/6pt0_20470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pt0_20470/07_2025/6pt0_20470.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.56, per 1000 atoms: 0.64 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: 2.44 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.21 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: 3.33 Time building geometry restraints manager: 2.85 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.670 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.790 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.033 0.002 TRP E 111 HIS 0.008 0.001 HIS E 35 PHE 0.020 0.002 PHE A 189 TYR 0.029 0.002 TYR A 74 ARG 0.005 0.000 ARG A 15 Details of bonding type rmsd hydrogen bonds : bond 0.10955 ( 529) hydrogen bonds : angle 6.16697 ( 1530) SS BOND : bond 0.00695 ( 2) SS BOND : angle 11.21410 ( 4) covalent geometry : bond 0.00606 (10450) covalent geometry : angle 0.88833 (14149) *********************** 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 : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 41 THR cc_start: 0.8831 (m) cc_final: 0.8475 (p) REVERT: R 56 TYR cc_start: 0.7524 (t80) cc_final: 0.7165 (t80) REVERT: R 65 ARG cc_start: 0.7497 (ttt180) cc_final: 0.6410 (mtm110) REVERT: R 130 ASP cc_start: 0.8801 (t70) cc_final: 0.8390 (t0) REVERT: R 146 THR cc_start: 0.7719 (m) cc_final: 0.7430 (p) REVERT: A 25 GLU cc_start: 0.8201 (tt0) cc_final: 0.7974 (tp30) REVERT: A 29 LYS cc_start: 0.8405 (ttmt) cc_final: 0.7997 (tptt) REVERT: A 224 CYS cc_start: 0.7694 (m) cc_final: 0.7475 (p) REVERT: A 330 LYS cc_start: 0.8346 (mmtt) cc_final: 0.7992 (pttm) REVERT: A 333 GLN cc_start: 0.8506 (tp40) cc_final: 0.7971 (tp-100) REVERT: B 7 LEU cc_start: 0.9003 (mm) cc_final: 0.8757 (mm) REVERT: B 9 GLN cc_start: 0.9273 (mm110) cc_final: 0.8641 (tm-30) REVERT: B 10 GLU cc_start: 0.9468 (tp30) cc_final: 0.9180 (tp30) REVERT: B 32 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8474 (tm-30) REVERT: B 101 MET cc_start: 0.9139 (mtp) cc_final: 0.8812 (mtp) REVERT: B 209 LYS cc_start: 0.8673 (mttm) cc_final: 0.8327 (mttt) REVERT: B 243 THR cc_start: 0.8994 (m) cc_final: 0.8465 (p) REVERT: B 258 ASP cc_start: 0.8495 (t70) cc_final: 0.8282 (t0) REVERT: C 20 LYS cc_start: 0.9498 (ttpt) cc_final: 0.9127 (mtpp) REVERT: C 42 GLU cc_start: 0.8664 (tt0) cc_final: 0.8429 (tp30) REVERT: E 52 SER cc_start: 0.8625 (m) cc_final: 0.8084 (t) REVERT: E 73 ASP cc_start: 0.7224 (t70) cc_final: 0.6760 (t70) REVERT: E 80 PHE cc_start: 0.7823 (m-80) cc_final: 0.7555 (m-80) REVERT: E 223 ASP cc_start: 0.8605 (m-30) cc_final: 0.7126 (m-30) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.2767 time to fit residues: 131.0184 Evaluate side-chains 193 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 chunk 60 optimal weight: 0.0470 chunk 74 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- 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 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.136590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.095143 restraints weight = 20049.905| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 3.44 r_work: 0.3278 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10452 Z= 0.132 Angle : 0.625 9.174 14153 Z= 0.315 Chirality : 0.042 0.187 1599 Planarity : 0.004 0.045 1761 Dihedral : 6.445 54.083 1728 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.85 % Allowed : 12.87 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.22), residues: 1272 helix: 0.79 (0.22), residues: 509 sheet: -1.26 (0.30), residues: 262 loop : -1.56 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 211 HIS 0.011 0.001 HIS B 54 PHE 0.016 0.001 PHE A 334 TYR 0.017 0.002 TYR E 190 ARG 0.007 0.001 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03505 ( 529) hydrogen bonds : angle 4.70942 ( 1530) SS BOND : bond 0.00241 ( 2) SS BOND : angle 1.33442 ( 4) covalent geometry : bond 0.00290 (10450) covalent geometry : angle 0.62504 (14149) *********************** 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 238 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 207 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 26 MET cc_start: 0.6269 (OUTLIER) cc_final: 0.5256 (tpt) REVERT: R 56 TYR cc_start: 0.7795 (t80) cc_final: 0.7350 (t80) REVERT: R 65 ARG cc_start: 0.7493 (ttt180) cc_final: 0.6409 (mtm110) REVERT: R 124 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8367 (mp) REVERT: R 130 ASP cc_start: 0.8859 (t70) cc_final: 0.8649 (t0) REVERT: R 146 THR cc_start: 0.8190 (m) cc_final: 0.7925 (p) REVERT: R 276 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8574 (pt0) REVERT: R 283 PHE cc_start: 0.7580 (m-80) cc_final: 0.7314 (m-10) REVERT: R 292 SER cc_start: 0.8845 (m) cc_final: 0.8552 (p) REVERT: A 224 CYS cc_start: 0.8569 (m) cc_final: 0.8141 (p) REVERT: A 243 MET cc_start: 0.9497 (tpp) cc_final: 0.9271 (mmm) REVERT: A 330 LYS cc_start: 0.8558 (mmtt) cc_final: 0.8284 (pttm) REVERT: B 10 GLU cc_start: 0.9491 (tp30) cc_final: 0.9289 (tp30) REVERT: B 101 MET cc_start: 0.9355 (mtp) cc_final: 0.9061 (mtp) REVERT: B 111 TYR cc_start: 0.9252 (m-80) cc_final: 0.9021 (m-80) REVERT: B 209 LYS cc_start: 0.8862 (mttm) cc_final: 0.8512 (mttp) REVERT: B 211 TRP cc_start: 0.9104 (m100) cc_final: 0.8679 (m100) REVERT: B 243 THR cc_start: 0.9177 (m) cc_final: 0.8960 (p) REVERT: B 247 ASP cc_start: 0.7602 (t0) cc_final: 0.7262 (t0) REVERT: B 258 ASP cc_start: 0.8586 (t70) cc_final: 0.8327 (t0) REVERT: B 289 TYR cc_start: 0.8480 (m-10) cc_final: 0.8116 (m-10) REVERT: B 297 TRP cc_start: 0.8592 (m100) cc_final: 0.8219 (m100) REVERT: C 13 ARG cc_start: 0.9347 (mtt-85) cc_final: 0.8782 (ptp-110) REVERT: C 20 LYS cc_start: 0.9518 (ttpt) cc_final: 0.9133 (ptmm) REVERT: C 29 LYS cc_start: 0.8851 (mmmt) cc_final: 0.8186 (tppt) REVERT: C 32 LYS cc_start: 0.9227 (tttt) cc_final: 0.8956 (tptp) REVERT: C 42 GLU cc_start: 0.8935 (tt0) cc_final: 0.8593 (tp30) REVERT: C 58 GLU cc_start: 0.8673 (pt0) cc_final: 0.8126 (pm20) REVERT: E 45 LEU cc_start: 0.8969 (mt) cc_final: 0.8748 (mt) REVERT: E 73 ASP cc_start: 0.7675 (t70) cc_final: 0.6738 (t70) REVERT: E 80 PHE cc_start: 0.8118 (m-80) cc_final: 0.7577 (m-80) REVERT: E 93 MET cc_start: 0.8742 (ttm) cc_final: 0.7996 (tpt) REVERT: E 148 PRO cc_start: 0.8998 (Cg_endo) cc_final: 0.8764 (Cg_exo) REVERT: E 220 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8266 (mp0) REVERT: E 223 ASP cc_start: 0.8451 (m-30) cc_final: 0.7266 (m-30) outliers start: 31 outliers final: 17 residues processed: 231 average time/residue: 0.2109 time to fit residues: 69.1139 Evaluate side-chains 196 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 124 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 239 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 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 327 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 239 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 99 optimal weight: 0.0970 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 16 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.133430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.091033 restraints weight = 20222.630| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.46 r_work: 0.3185 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3358 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= 0.135 Angle : 0.585 10.069 14153 Z= 0.294 Chirality : 0.041 0.143 1599 Planarity : 0.004 0.045 1761 Dihedral : 5.977 55.766 1728 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.03 % Allowed : 14.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.23), residues: 1272 helix: 1.51 (0.23), residues: 508 sheet: -1.16 (0.30), residues: 276 loop : -1.23 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 131 HIS 0.005 0.001 HIS E 232 PHE 0.009 0.001 PHE A 189 TYR 0.014 0.001 TYR E 190 ARG 0.005 0.000 ARG R 229 Details of bonding type rmsd hydrogen bonds : bond 0.03323 ( 529) hydrogen bonds : angle 4.45599 ( 1530) SS BOND : bond 0.00309 ( 2) SS BOND : angle 0.90296 ( 4) covalent geometry : bond 0.00304 (10450) covalent geometry : angle 0.58533 (14149) *********************** 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 213 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 26 MET cc_start: 0.6407 (mmm) cc_final: 0.5758 (tpp) REVERT: R 56 TYR cc_start: 0.8029 (t80) cc_final: 0.7580 (t80) REVERT: R 65 ARG cc_start: 0.7505 (ttt180) cc_final: 0.6415 (mtm110) REVERT: R 124 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8287 (mp) REVERT: R 130 ASP cc_start: 0.8820 (t70) cc_final: 0.8569 (t0) REVERT: R 132 TYR cc_start: 0.8150 (t80) cc_final: 0.7870 (t80) REVERT: R 239 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7442 (pp) REVERT: R 276 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8542 (pt0) REVERT: R 283 PHE cc_start: 0.7605 (m-80) cc_final: 0.7346 (m-10) REVERT: R 292 SER cc_start: 0.8941 (m) cc_final: 0.8646 (p) REVERT: R 313 CYS cc_start: 0.7440 (OUTLIER) cc_final: 0.6979 (p) REVERT: A 53 MET cc_start: 0.8366 (mtm) cc_final: 0.7817 (mtm) REVERT: A 198 MET cc_start: 0.8404 (tpp) cc_final: 0.8194 (ttm) REVERT: A 224 CYS cc_start: 0.8827 (m) cc_final: 0.8311 (p) REVERT: A 330 LYS cc_start: 0.8707 (mmtt) cc_final: 0.8237 (ptmt) REVERT: B 10 GLU cc_start: 0.9539 (tp30) cc_final: 0.9297 (tp30) REVERT: B 101 MET cc_start: 0.9362 (mtp) cc_final: 0.9080 (mtp) REVERT: B 209 LYS cc_start: 0.8869 (mttm) cc_final: 0.8571 (mttt) REVERT: B 211 TRP cc_start: 0.9138 (m100) cc_final: 0.8899 (m100) REVERT: B 258 ASP cc_start: 0.8626 (t70) cc_final: 0.8382 (t0) REVERT: B 289 TYR cc_start: 0.8625 (m-10) cc_final: 0.8317 (m-80) REVERT: B 297 TRP cc_start: 0.8855 (m100) cc_final: 0.8239 (m100) REVERT: C 13 ARG cc_start: 0.9419 (mtt-85) cc_final: 0.8848 (ptp-110) REVERT: C 20 LYS cc_start: 0.9513 (ttpt) cc_final: 0.9124 (ptmm) REVERT: C 29 LYS cc_start: 0.8863 (mmmt) cc_final: 0.8623 (mmmt) REVERT: C 32 LYS cc_start: 0.9300 (tttt) cc_final: 0.8987 (tptp) REVERT: C 42 GLU cc_start: 0.8973 (tt0) cc_final: 0.8559 (tp30) REVERT: C 58 GLU cc_start: 0.8762 (pt0) cc_final: 0.7953 (pm20) REVERT: E 51 ILE cc_start: 0.8359 (mp) cc_final: 0.8064 (mp) REVERT: E 73 ASP cc_start: 0.7815 (t70) cc_final: 0.6350 (t70) REVERT: E 80 PHE cc_start: 0.8158 (m-80) cc_final: 0.7607 (m-80) REVERT: E 93 MET cc_start: 0.8721 (ttm) cc_final: 0.8072 (tpt) REVERT: E 220 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8159 (mp0) REVERT: E 223 ASP cc_start: 0.8541 (m-30) cc_final: 0.6955 (m-30) outliers start: 33 outliers final: 15 residues processed: 205 average time/residue: 0.2034 time to fit residues: 59.7197 Evaluate side-chains 182 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 267 HIS Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 313 CYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 110 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 15 optimal weight: 20.0000 chunk 94 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** 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 = 0.3905 r_free = 0.3905 target = 0.124576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.080601 restraints weight = 20083.152| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.33 r_work: 0.2997 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 10452 Z= 0.238 Angle : 0.641 7.827 14153 Z= 0.325 Chirality : 0.044 0.157 1599 Planarity : 0.004 0.045 1761 Dihedral : 6.136 57.081 1728 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.22 % Allowed : 14.25 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.24), residues: 1272 helix: 1.57 (0.23), residues: 515 sheet: -0.94 (0.30), residues: 273 loop : -1.10 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 99 HIS 0.009 0.001 HIS E 232 PHE 0.022 0.002 PHE E 239 TYR 0.022 0.002 TYR E 103 ARG 0.013 0.001 ARG R 229 Details of bonding type rmsd hydrogen bonds : bond 0.03541 ( 529) hydrogen bonds : angle 4.51562 ( 1530) SS BOND : bond 0.00135 ( 2) SS BOND : angle 0.61362 ( 4) covalent geometry : bond 0.00541 (10450) covalent geometry : angle 0.64120 (14149) *********************** 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 201 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 26 MET cc_start: 0.6625 (OUTLIER) cc_final: 0.6363 (tpp) REVERT: R 56 TYR cc_start: 0.8195 (t80) cc_final: 0.7662 (t80) REVERT: R 65 ARG cc_start: 0.7604 (ttt180) cc_final: 0.6488 (mtm110) REVERT: R 124 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8348 (mp) REVERT: R 130 ASP cc_start: 0.8916 (t70) cc_final: 0.8683 (t0) REVERT: R 207 TYR cc_start: 0.7916 (t80) cc_final: 0.7489 (t80) REVERT: R 240 ASP cc_start: 0.8524 (t0) cc_final: 0.8286 (t0) REVERT: R 276 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8262 (pt0) REVERT: R 292 SER cc_start: 0.9150 (m) cc_final: 0.8821 (p) REVERT: R 305 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7748 (tm-30) REVERT: R 313 CYS cc_start: 0.7457 (OUTLIER) cc_final: 0.6891 (p) REVERT: A 224 CYS cc_start: 0.9049 (m) cc_final: 0.8315 (p) REVERT: A 330 LYS cc_start: 0.8741 (mmtt) cc_final: 0.8310 (ptmt) REVERT: B 7 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8584 (mm) REVERT: B 10 GLU cc_start: 0.9513 (tp30) cc_final: 0.9268 (tp30) REVERT: B 101 MET cc_start: 0.9304 (mtp) cc_final: 0.9041 (mtp) REVERT: B 209 LYS cc_start: 0.9047 (mttm) cc_final: 0.8825 (mttp) REVERT: B 258 ASP cc_start: 0.8782 (t70) cc_final: 0.8447 (t0) REVERT: B 280 LYS cc_start: 0.9210 (mtpp) cc_final: 0.9010 (mtpp) REVERT: B 297 TRP cc_start: 0.9119 (m100) cc_final: 0.8174 (m100) REVERT: C 13 ARG cc_start: 0.9386 (mtt-85) cc_final: 0.8796 (ptp-110) REVERT: C 20 LYS cc_start: 0.9501 (ttpt) cc_final: 0.9100 (ptmm) REVERT: C 29 LYS cc_start: 0.8978 (mmmt) cc_final: 0.8772 (mmmt) REVERT: C 42 GLU cc_start: 0.9076 (tt0) cc_final: 0.8812 (tm-30) REVERT: C 58 GLU cc_start: 0.8773 (pt0) cc_final: 0.8141 (pm20) REVERT: E 73 ASP cc_start: 0.7849 (t70) cc_final: 0.7204 (t70) REVERT: E 93 MET cc_start: 0.8745 (ttm) cc_final: 0.8020 (tpt) REVERT: E 140 MET cc_start: 0.9234 (mmm) cc_final: 0.8743 (mmm) REVERT: E 220 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8561 (mm-30) REVERT: E 223 ASP cc_start: 0.8578 (m-30) cc_final: 0.8060 (m-30) outliers start: 35 outliers final: 25 residues processed: 189 average time/residue: 0.2249 time to fit residues: 60.6189 Evaluate side-chains 178 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 1.222 ------------------------------------------------------------------------------- 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 124 LEU 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 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 B residue 7 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 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 C residue 21 MET Chi-restraints excluded: chain E residue 2 VAL 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 123 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 41 optimal weight: 30.0000 chunk 14 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 58 optimal weight: 20.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 244 HIS ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN ** B 239 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 = 0.3895 r_free = 0.3895 target = 0.124175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.080227 restraints weight = 19946.998| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.29 r_work: 0.2985 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 10452 Z= 0.203 Angle : 0.606 7.259 14153 Z= 0.308 Chirality : 0.042 0.169 1599 Planarity : 0.004 0.043 1761 Dihedral : 6.272 56.977 1728 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.04 % Allowed : 14.71 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.24), residues: 1272 helix: 1.78 (0.23), residues: 509 sheet: -0.68 (0.30), residues: 267 loop : -1.14 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.006 0.001 HIS E 232 PHE 0.016 0.002 PHE B 278 TYR 0.019 0.002 TYR E 103 ARG 0.007 0.000 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.03383 ( 529) hydrogen bonds : angle 4.43794 ( 1530) SS BOND : bond 0.00157 ( 2) SS BOND : angle 0.44104 ( 4) covalent geometry : bond 0.00462 (10450) covalent geometry : angle 0.60653 (14149) *********************** 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 204 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 160 time to evaluate : 1.125 Fit side-chains revert: symmetry clash REVERT: R 26 MET cc_start: 0.6748 (OUTLIER) cc_final: 0.6545 (tpp) REVERT: R 56 TYR cc_start: 0.8310 (t80) cc_final: 0.7660 (t80) REVERT: R 65 ARG cc_start: 0.7748 (ttt180) cc_final: 0.6600 (mtm110) REVERT: R 124 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8340 (mp) REVERT: R 207 TYR cc_start: 0.7916 (t80) cc_final: 0.7366 (t80) REVERT: R 276 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8311 (pt0) REVERT: R 292 SER cc_start: 0.9295 (m) cc_final: 0.8945 (p) REVERT: R 305 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7793 (tm-30) REVERT: R 313 CYS cc_start: 0.7532 (OUTLIER) cc_final: 0.6944 (p) REVERT: A 224 CYS cc_start: 0.8979 (m) cc_final: 0.8343 (p) REVERT: A 330 LYS cc_start: 0.8788 (mmtt) cc_final: 0.8389 (ptmt) REVERT: B 7 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8601 (mm) REVERT: B 10 GLU cc_start: 0.9519 (tp30) cc_final: 0.9310 (tp30) REVERT: B 101 MET cc_start: 0.9280 (mtp) cc_final: 0.9026 (mtp) REVERT: B 209 LYS cc_start: 0.9020 (mttm) cc_final: 0.8802 (mttp) REVERT: B 258 ASP cc_start: 0.8676 (t70) cc_final: 0.8390 (t0) REVERT: C 16 VAL cc_start: 0.9320 (t) cc_final: 0.9102 (m) REVERT: C 20 LYS cc_start: 0.9481 (ttpt) cc_final: 0.9095 (mtpp) REVERT: C 29 LYS cc_start: 0.8965 (mmmt) cc_final: 0.8680 (mmmt) REVERT: C 58 GLU cc_start: 0.8786 (pt0) cc_final: 0.8175 (pm20) REVERT: E 51 ILE cc_start: 0.8364 (mp) cc_final: 0.8086 (mp) REVERT: E 73 ASP cc_start: 0.7921 (t70) cc_final: 0.7307 (t70) REVERT: E 82 GLN cc_start: 0.8295 (tp-100) cc_final: 0.8031 (tp-100) REVERT: E 93 MET cc_start: 0.8698 (ttm) cc_final: 0.8024 (tpt) REVERT: E 223 ASP cc_start: 0.8663 (m-30) cc_final: 0.8119 (m-30) outliers start: 44 outliers final: 30 residues processed: 187 average time/residue: 0.2085 time to fit residues: 55.5911 Evaluate side-chains 186 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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 124 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 247 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 20 ASP 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 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 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 41 optimal weight: 8.9990 chunk 34 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 109 optimal weight: 0.6980 chunk 120 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.126067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.081592 restraints weight = 20045.559| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 3.37 r_work: 0.3010 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10452 Z= 0.143 Angle : 0.577 7.022 14153 Z= 0.292 Chirality : 0.041 0.161 1599 Planarity : 0.003 0.043 1761 Dihedral : 6.093 56.789 1728 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.58 % Allowed : 16.27 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.24), residues: 1272 helix: 1.85 (0.23), residues: 510 sheet: -0.67 (0.30), residues: 261 loop : -1.06 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.005 0.001 HIS E 232 PHE 0.013 0.001 PHE B 278 TYR 0.015 0.001 TYR E 103 ARG 0.006 0.000 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.03215 ( 529) hydrogen bonds : angle 4.35199 ( 1530) SS BOND : bond 0.00161 ( 2) SS BOND : angle 0.41238 ( 4) covalent geometry : bond 0.00324 (10450) covalent geometry : angle 0.57746 (14149) *********************** 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 202 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 1.302 Fit side-chains revert: symmetry clash REVERT: R 49 LEU cc_start: 0.8768 (mt) cc_final: 0.8506 (tp) REVERT: R 56 TYR cc_start: 0.8340 (t80) cc_final: 0.7863 (t80) REVERT: R 65 ARG cc_start: 0.7714 (ttt180) cc_final: 0.6578 (mtm110) REVERT: R 70 TYR cc_start: 0.8762 (m-80) cc_final: 0.8506 (m-80) REVERT: R 124 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8314 (mp) REVERT: R 207 TYR cc_start: 0.7915 (t80) cc_final: 0.7436 (t80) REVERT: R 239 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7449 (pp) REVERT: R 276 GLN cc_start: 0.8769 (mm-40) cc_final: 0.8271 (pt0) REVERT: R 292 SER cc_start: 0.9273 (m) cc_final: 0.8911 (p) REVERT: R 305 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7667 (tm-30) REVERT: R 313 CYS cc_start: 0.7471 (t) cc_final: 0.6959 (p) REVERT: A 224 CYS cc_start: 0.8968 (m) cc_final: 0.8354 (p) REVERT: A 330 LYS cc_start: 0.8780 (mmtt) cc_final: 0.8375 (ptmt) REVERT: B 10 GLU cc_start: 0.9513 (tp30) cc_final: 0.9299 (tp30) REVERT: B 59 TYR cc_start: 0.9156 (m-80) cc_final: 0.8930 (m-80) REVERT: B 101 MET cc_start: 0.9246 (mtp) cc_final: 0.8996 (mtp) REVERT: B 209 LYS cc_start: 0.8937 (mttm) cc_final: 0.8586 (mttt) REVERT: B 258 ASP cc_start: 0.8550 (t70) cc_final: 0.8311 (t0) REVERT: B 289 TYR cc_start: 0.8796 (m-80) cc_final: 0.8577 (m-80) REVERT: B 297 TRP cc_start: 0.9142 (m100) cc_final: 0.8327 (m100) REVERT: C 20 LYS cc_start: 0.9472 (ttpt) cc_final: 0.9083 (mtpp) REVERT: C 29 LYS cc_start: 0.8962 (mmmt) cc_final: 0.8743 (mmmt) REVERT: C 58 GLU cc_start: 0.8823 (pt0) cc_final: 0.8196 (pm20) REVERT: E 73 ASP cc_start: 0.7852 (t70) cc_final: 0.7191 (t0) REVERT: E 82 GLN cc_start: 0.8162 (tp-100) cc_final: 0.7942 (tp-100) REVERT: E 83 MET cc_start: 0.8929 (mtm) cc_final: 0.8667 (mtm) REVERT: E 93 MET cc_start: 0.8678 (ttm) cc_final: 0.8128 (tpt) REVERT: E 223 ASP cc_start: 0.8626 (m-30) cc_final: 0.8184 (m-30) outliers start: 39 outliers final: 25 residues processed: 188 average time/residue: 0.2230 time to fit residues: 60.1003 Evaluate side-chains 182 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 CYS Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 124 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 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 243 THR 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 C residue 51 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 117 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 55 optimal weight: 0.0980 chunk 5 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 112 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 218 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.127458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.084647 restraints weight = 20175.423| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.32 r_work: 0.3075 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10452 Z= 0.110 Angle : 0.567 8.182 14153 Z= 0.283 Chirality : 0.041 0.200 1599 Planarity : 0.003 0.043 1761 Dihedral : 5.857 57.311 1728 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.21 % Allowed : 18.01 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.24), residues: 1272 helix: 1.98 (0.23), residues: 510 sheet: -0.62 (0.30), residues: 271 loop : -0.99 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS B 225 PHE 0.010 0.001 PHE A 189 TYR 0.013 0.001 TYR E 190 ARG 0.005 0.000 ARG C 13 Details of bonding type rmsd hydrogen bonds : bond 0.03067 ( 529) hydrogen bonds : angle 4.26348 ( 1530) SS BOND : bond 0.00204 ( 2) SS BOND : angle 0.56716 ( 4) covalent geometry : bond 0.00241 (10450) covalent geometry : angle 0.56687 (14149) *********************** 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 195 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 49 LEU cc_start: 0.8773 (mt) cc_final: 0.8518 (tp) REVERT: R 56 TYR cc_start: 0.8257 (t80) cc_final: 0.7842 (t80) REVERT: R 65 ARG cc_start: 0.7712 (ttt180) cc_final: 0.6575 (mtm110) REVERT: R 70 TYR cc_start: 0.8635 (m-80) cc_final: 0.8388 (m-80) REVERT: R 124 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8297 (mp) REVERT: R 146 THR cc_start: 0.8117 (OUTLIER) cc_final: 0.7917 (p) REVERT: R 207 TYR cc_start: 0.7866 (t80) cc_final: 0.7267 (t80) REVERT: R 239 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.6976 (pp) REVERT: R 276 GLN cc_start: 0.8745 (mm-40) cc_final: 0.8207 (pt0) REVERT: R 292 SER cc_start: 0.9272 (m) cc_final: 0.8928 (p) REVERT: R 305 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7822 (tm-30) REVERT: R 313 CYS cc_start: 0.7446 (t) cc_final: 0.7107 (p) REVERT: A 193 ASP cc_start: 0.7862 (t0) cc_final: 0.7287 (t0) REVERT: A 330 LYS cc_start: 0.8825 (mmtt) cc_final: 0.8373 (ptmt) REVERT: B 10 GLU cc_start: 0.9478 (tp30) cc_final: 0.9235 (tp30) REVERT: B 59 TYR cc_start: 0.9090 (m-80) cc_final: 0.8786 (m-80) REVERT: B 101 MET cc_start: 0.9121 (mtp) cc_final: 0.8916 (mtp) REVERT: B 207 SER cc_start: 0.8920 (m) cc_final: 0.8375 (p) REVERT: B 209 LYS cc_start: 0.8795 (mttm) cc_final: 0.8590 (mttt) REVERT: B 214 ARG cc_start: 0.8769 (mmt180) cc_final: 0.8417 (mmt180) REVERT: B 258 ASP cc_start: 0.8498 (t70) cc_final: 0.8283 (t0) REVERT: B 297 TRP cc_start: 0.9035 (m100) cc_final: 0.8355 (m100) REVERT: C 20 LYS cc_start: 0.9482 (ttpt) cc_final: 0.9100 (mtpp) REVERT: C 58 GLU cc_start: 0.8775 (pt0) cc_final: 0.8180 (pm20) REVERT: E 73 ASP cc_start: 0.7858 (t70) cc_final: 0.7216 (t0) REVERT: E 83 MET cc_start: 0.8806 (mtm) cc_final: 0.8512 (mtm) REVERT: E 93 MET cc_start: 0.8571 (ttm) cc_final: 0.8117 (tpt) REVERT: E 223 ASP cc_start: 0.8527 (m-30) cc_final: 0.8252 (m-30) outliers start: 24 outliers final: 14 residues processed: 187 average time/residue: 0.2293 time to fit residues: 60.6601 Evaluate side-chains 175 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 312 HIS 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 243 THR Chi-restraints excluded: chain B residue 278 PHE 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 11 LEU Chi-restraints excluded: chain E residue 69 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 0 optimal weight: 40.0000 chunk 56 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 98 HIS ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.122577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.078419 restraints weight = 20279.496| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.27 r_work: 0.2946 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 10452 Z= 0.244 Angle : 0.657 8.913 14153 Z= 0.329 Chirality : 0.043 0.177 1599 Planarity : 0.004 0.088 1761 Dihedral : 6.328 59.699 1728 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.31 % Allowed : 18.11 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.24), residues: 1272 helix: 1.85 (0.22), residues: 507 sheet: -0.60 (0.31), residues: 267 loop : -0.99 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 339 HIS 0.005 0.001 HIS C 44 PHE 0.019 0.002 PHE B 292 TYR 0.015 0.002 TYR B 289 ARG 0.012 0.001 ARG A 242 Details of bonding type rmsd hydrogen bonds : bond 0.03445 ( 529) hydrogen bonds : angle 4.47213 ( 1530) SS BOND : bond 0.00143 ( 2) SS BOND : angle 0.36641 ( 4) covalent geometry : bond 0.00554 (10450) covalent geometry : angle 0.65700 (14149) *********************** 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 188 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: R 49 LEU cc_start: 0.8802 (mt) cc_final: 0.8541 (tp) REVERT: R 65 ARG cc_start: 0.7677 (ttt180) cc_final: 0.6493 (mtm110) REVERT: R 70 TYR cc_start: 0.8818 (m-80) cc_final: 0.8574 (m-80) REVERT: R 124 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8333 (mp) REVERT: R 207 TYR cc_start: 0.7958 (t80) cc_final: 0.7383 (t80) REVERT: R 276 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8275 (pt0) REVERT: R 292 SER cc_start: 0.9355 (m) cc_final: 0.8979 (p) REVERT: R 305 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7752 (tm-30) REVERT: R 313 CYS cc_start: 0.7495 (t) cc_final: 0.6958 (p) REVERT: A 330 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8419 (ptmt) REVERT: B 10 GLU cc_start: 0.9473 (tp30) cc_final: 0.9250 (tp30) REVERT: B 101 MET cc_start: 0.9262 (mtp) cc_final: 0.8985 (mtp) REVERT: B 207 SER cc_start: 0.8864 (m) cc_final: 0.8322 (p) REVERT: B 209 LYS cc_start: 0.8968 (mttm) cc_final: 0.8759 (mttp) REVERT: B 258 ASP cc_start: 0.8561 (t70) cc_final: 0.8341 (t0) REVERT: C 58 GLU cc_start: 0.8834 (pt0) cc_final: 0.8065 (pm20) REVERT: E 51 ILE cc_start: 0.8222 (mp) cc_final: 0.7795 (tt) REVERT: E 73 ASP cc_start: 0.8006 (t70) cc_final: 0.7349 (t0) REVERT: E 93 MET cc_start: 0.8830 (ttm) cc_final: 0.8094 (tpt) REVERT: E 223 ASP cc_start: 0.8572 (m-30) cc_final: 0.8299 (m-30) REVERT: E 234 GLU cc_start: 0.8487 (pt0) cc_final: 0.8287 (pm20) outliers start: 36 outliers final: 27 residues processed: 177 average time/residue: 0.2085 time to fit residues: 52.7867 Evaluate side-chains 177 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 124 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 294 VAL Chi-restraints excluded: chain R residue 312 HIS 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 243 THR 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 C residue 21 MET Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 42 optimal weight: 30.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 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 = 0.3895 r_free = 0.3895 target = 0.124319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.080701 restraints weight = 20303.423| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.28 r_work: 0.2990 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10452 Z= 0.163 Angle : 0.630 10.927 14153 Z= 0.312 Chirality : 0.042 0.156 1599 Planarity : 0.004 0.054 1761 Dihedral : 6.253 59.019 1728 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.39 % Allowed : 19.03 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.24), residues: 1272 helix: 1.89 (0.22), residues: 508 sheet: -0.49 (0.31), residues: 271 loop : -1.03 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 99 HIS 0.004 0.001 HIS C 44 PHE 0.012 0.001 PHE B 278 TYR 0.014 0.001 TYR E 103 ARG 0.006 0.000 ARG C 13 Details of bonding type rmsd hydrogen bonds : bond 0.03243 ( 529) hydrogen bonds : angle 4.37711 ( 1530) SS BOND : bond 0.00216 ( 2) SS BOND : angle 0.41123 ( 4) covalent geometry : bond 0.00374 (10450) covalent geometry : angle 0.63027 (14149) *********************** 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 185 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 1.274 Fit side-chains revert: symmetry clash REVERT: R 49 LEU cc_start: 0.8830 (mt) cc_final: 0.8569 (tp) REVERT: R 56 TYR cc_start: 0.8350 (t80) cc_final: 0.7905 (t80) REVERT: R 65 ARG cc_start: 0.7710 (ttt180) cc_final: 0.6553 (mtm110) REVERT: R 70 TYR cc_start: 0.8761 (m-80) cc_final: 0.8496 (m-80) REVERT: R 124 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8324 (mp) REVERT: R 207 TYR cc_start: 0.7931 (t80) cc_final: 0.7354 (t80) REVERT: R 275 ASP cc_start: 0.8700 (p0) cc_final: 0.8489 (p0) REVERT: R 292 SER cc_start: 0.9358 (m) cc_final: 0.8982 (p) REVERT: R 305 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7715 (tm-30) REVERT: R 313 CYS cc_start: 0.7452 (t) cc_final: 0.6996 (p) REVERT: A 330 LYS cc_start: 0.8827 (mmtt) cc_final: 0.8393 (ptmt) REVERT: B 10 GLU cc_start: 0.9471 (tp30) cc_final: 0.9247 (tp30) REVERT: B 101 MET cc_start: 0.9198 (mtp) cc_final: 0.8943 (mtp) REVERT: B 207 SER cc_start: 0.8936 (m) cc_final: 0.8387 (p) REVERT: B 280 LYS cc_start: 0.9005 (mtpp) cc_final: 0.8754 (mtpp) REVERT: B 297 TRP cc_start: 0.9151 (m100) cc_final: 0.8277 (m100) REVERT: C 13 ARG cc_start: 0.9278 (ttm110) cc_final: 0.8996 (ttm-80) REVERT: C 20 LYS cc_start: 0.9336 (ttmm) cc_final: 0.8880 (mtpp) REVERT: C 58 GLU cc_start: 0.8822 (pt0) cc_final: 0.8182 (pm20) REVERT: E 51 ILE cc_start: 0.8092 (mp) cc_final: 0.7597 (tt) REVERT: E 73 ASP cc_start: 0.7867 (t70) cc_final: 0.7241 (t0) REVERT: E 93 MET cc_start: 0.8676 (ttm) cc_final: 0.8027 (tpt) REVERT: E 223 ASP cc_start: 0.8507 (m-30) cc_final: 0.8248 (m-30) outliers start: 26 outliers final: 24 residues processed: 177 average time/residue: 0.2665 time to fit residues: 67.2676 Evaluate side-chains 180 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 124 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 A residue 184 ILE 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 C residue 21 MET Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 82 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 110 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 101 optimal weight: 0.0170 chunk 32 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 57 optimal weight: 0.4980 chunk 105 optimal weight: 10.0000 overall best weight: 2.0822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 276 GLN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 239 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 = 0.3883 r_free = 0.3883 target = 0.123445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.079815 restraints weight = 20170.098| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 3.26 r_work: 0.2986 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10452 Z= 0.183 Angle : 0.661 12.636 14153 Z= 0.327 Chirality : 0.042 0.164 1599 Planarity : 0.004 0.041 1761 Dihedral : 6.318 59.906 1728 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.67 % Allowed : 18.57 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.24), residues: 1272 helix: 1.91 (0.22), residues: 508 sheet: -0.41 (0.31), residues: 261 loop : -1.04 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 339 HIS 0.004 0.001 HIS C 44 PHE 0.014 0.001 PHE B 278 TYR 0.014 0.001 TYR E 103 ARG 0.007 0.001 ARG A 86 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 529) hydrogen bonds : angle 4.42237 ( 1530) SS BOND : bond 0.00217 ( 2) SS BOND : angle 0.42225 ( 4) covalent geometry : bond 0.00421 (10450) covalent geometry : angle 0.66079 (14149) ********************** 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 184 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: R 26 MET cc_start: 0.6513 (tpp) cc_final: 0.6280 (tpp) REVERT: R 49 LEU cc_start: 0.8855 (mt) cc_final: 0.8594 (tp) REVERT: R 56 TYR cc_start: 0.8380 (t80) cc_final: 0.7771 (t80) REVERT: R 65 ARG cc_start: 0.7721 (ttt180) cc_final: 0.6553 (mtm110) REVERT: R 70 TYR cc_start: 0.8753 (m-80) cc_final: 0.8453 (m-80) REVERT: R 124 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8332 (mp) REVERT: R 207 TYR cc_start: 0.7954 (t80) cc_final: 0.7381 (t80) REVERT: R 292 SER cc_start: 0.9355 (m) cc_final: 0.8974 (p) REVERT: R 305 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7723 (tm-30) REVERT: R 313 CYS cc_start: 0.7481 (t) cc_final: 0.6982 (p) REVERT: A 330 LYS cc_start: 0.8831 (mmtt) cc_final: 0.8401 (ptmt) REVERT: B 10 GLU cc_start: 0.9468 (tp30) cc_final: 0.9246 (tp30) REVERT: B 16 ASN cc_start: 0.9308 (m110) cc_final: 0.9032 (p0) REVERT: B 101 MET cc_start: 0.9216 (mtp) cc_final: 0.8957 (mtp) REVERT: B 207 SER cc_start: 0.9016 (m) cc_final: 0.8450 (p) REVERT: B 217 MET cc_start: 0.8658 (ppp) cc_final: 0.8151 (ppp) REVERT: B 280 LYS cc_start: 0.9025 (mtpp) cc_final: 0.8767 (mtpp) REVERT: B 297 TRP cc_start: 0.9142 (m100) cc_final: 0.8264 (m100) REVERT: B 339 TRP cc_start: 0.9057 (m100) cc_final: 0.8614 (m100) REVERT: C 13 ARG cc_start: 0.9296 (ttm110) cc_final: 0.9020 (ttm-80) REVERT: C 20 LYS cc_start: 0.9344 (ttmm) cc_final: 0.8877 (mtpp) REVERT: C 58 GLU cc_start: 0.8871 (pt0) cc_final: 0.8221 (pm20) REVERT: E 51 ILE cc_start: 0.8061 (mp) cc_final: 0.7565 (tt) REVERT: E 73 ASP cc_start: 0.7943 (t70) cc_final: 0.7334 (t0) REVERT: E 93 MET cc_start: 0.8706 (ttm) cc_final: 0.8033 (tpt) REVERT: E 223 ASP cc_start: 0.8536 (m-30) cc_final: 0.8285 (m-30) outliers start: 29 outliers final: 25 residues processed: 175 average time/residue: 0.2144 time to fit residues: 53.9588 Evaluate side-chains 179 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 124 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 239 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 A residue 184 ILE 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 C residue 21 MET Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 51 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 117 optimal weight: 9.9990 chunk 44 optimal weight: 30.0000 chunk 7 optimal weight: 20.0000 chunk 81 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 84 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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** ** B 239 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 = 0.3879 r_free = 0.3879 target = 0.123160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.079420 restraints weight = 20066.807| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.24 r_work: 0.2973 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.5517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10452 Z= 0.187 Angle : 0.661 11.293 14153 Z= 0.328 Chirality : 0.043 0.172 1599 Planarity : 0.004 0.040 1761 Dihedral : 6.349 60.615 1728 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.85 % Allowed : 18.57 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.24), residues: 1272 helix: 1.91 (0.22), residues: 508 sheet: -0.35 (0.32), residues: 259 loop : -1.01 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 339 HIS 0.004 0.001 HIS C 44 PHE 0.014 0.001 PHE B 278 TYR 0.014 0.001 TYR E 103 ARG 0.007 0.001 ARG A 86 Details of bonding type rmsd hydrogen bonds : bond 0.03323 ( 529) hydrogen bonds : angle 4.45817 ( 1530) SS BOND : bond 0.00231 ( 2) SS BOND : angle 0.42504 ( 4) covalent geometry : bond 0.00433 (10450) covalent geometry : angle 0.66127 (14149) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6017.16 seconds wall clock time: 106 minutes 23.83 seconds (6383.83 seconds total)