Starting phenix.real_space_refine on Fri Feb 14 17:23:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pt0_20470/02_2025/6pt0_20470.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pt0_20470/02_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_20470/02_2025/6pt0_20470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pt0_20470/02_2025/6pt0_20470.map" model { file = "/net/cci-nas-00/data/ceres_data/6pt0_20470/02_2025/6pt0_20470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pt0_20470/02_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-5592/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: 6.04, per 1000 atoms: 0.59 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: 2.61 Conformation dependent library (CDL) restraints added in 1.2 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: 1.11 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: 3.06 Time building geometry restraints manager: 2.94 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: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.510 Find NCS groups from input model: 0.160 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: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.300 ------------------------------------------------------------------------------- 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 10450 Z= 0.437 Angle : 0.888 9.556 14149 Z= 0.454 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 *********************** 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 : 1.181 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: 0.2733 time to fit residues: 128.8752 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 : 1.184 ------------------------------------------------------------------------------- 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 = 0.4071 r_free = 0.4071 target = 0.136591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.095144 restraints weight = 20049.648| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 3.44 r_work: 0.3278 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 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 10450 Z= 0.187 Angle : 0.625 9.175 14149 Z= 0.315 Chirality : 0.042 0.187 1599 Planarity : 0.004 0.045 1761 Dihedral : 6.446 54.084 1728 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.76 % Allowed : 12.96 % 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: -1.25 (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 *********************** 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 237 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 26 MET cc_start: 0.6268 (OUTLIER) cc_final: 0.5256 (tpt) REVERT: R 56 TYR cc_start: 0.7793 (t80) cc_final: 0.7350 (t80) REVERT: R 65 ARG cc_start: 0.7494 (ttt180) cc_final: 0.6412 (mtm110) REVERT: R 124 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8368 (mp) REVERT: R 130 ASP cc_start: 0.8860 (t70) cc_final: 0.8651 (t0) REVERT: R 146 THR cc_start: 0.8191 (m) cc_final: 0.7926 (p) REVERT: R 276 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8573 (pt0) REVERT: R 283 PHE cc_start: 0.7580 (m-80) cc_final: 0.7316 (m-10) REVERT: R 292 SER cc_start: 0.8847 (m) cc_final: 0.8554 (p) REVERT: A 224 CYS cc_start: 0.8571 (m) cc_final: 0.8145 (p) REVERT: A 243 MET cc_start: 0.9497 (tpp) cc_final: 0.9273 (mmm) REVERT: A 330 LYS cc_start: 0.8556 (mmtt) cc_final: 0.8283 (pttm) REVERT: B 10 GLU cc_start: 0.9489 (tp30) cc_final: 0.9288 (tp30) REVERT: B 101 MET cc_start: 0.9353 (mtp) cc_final: 0.9059 (mtp) REVERT: B 111 TYR cc_start: 0.9251 (m-80) cc_final: 0.9021 (m-80) REVERT: B 209 LYS cc_start: 0.8864 (mttm) cc_final: 0.8514 (mttp) REVERT: B 211 TRP cc_start: 0.9104 (m100) cc_final: 0.8680 (m100) REVERT: B 243 THR cc_start: 0.9175 (m) cc_final: 0.8958 (p) REVERT: B 247 ASP cc_start: 0.7603 (t0) cc_final: 0.7263 (t0) REVERT: B 258 ASP cc_start: 0.8589 (t70) cc_final: 0.8330 (t0) REVERT: B 289 TYR cc_start: 0.8482 (m-10) cc_final: 0.8119 (m-10) REVERT: B 297 TRP cc_start: 0.8595 (m100) cc_final: 0.8219 (m100) REVERT: C 13 ARG cc_start: 0.9347 (mtt-85) cc_final: 0.8783 (ptp-110) REVERT: C 20 LYS cc_start: 0.9518 (ttpt) cc_final: 0.9134 (ptmm) REVERT: C 29 LYS cc_start: 0.8850 (mmmt) cc_final: 0.8185 (tppt) REVERT: C 32 LYS cc_start: 0.9226 (tttt) cc_final: 0.8955 (tptp) REVERT: C 42 GLU cc_start: 0.8927 (tt0) cc_final: 0.8589 (tp30) REVERT: C 58 GLU cc_start: 0.8676 (pt0) cc_final: 0.8127 (pm20) REVERT: E 45 LEU cc_start: 0.8969 (mt) cc_final: 0.8748 (mt) REVERT: E 73 ASP cc_start: 0.7673 (t70) cc_final: 0.6733 (t70) REVERT: E 80 PHE cc_start: 0.8118 (m-80) cc_final: 0.7575 (m-80) REVERT: E 93 MET cc_start: 0.8742 (ttm) cc_final: 0.7995 (tpt) REVERT: E 148 PRO cc_start: 0.8995 (Cg_endo) cc_final: 0.8760 (Cg_exo) REVERT: E 220 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8269 (mp0) REVERT: E 223 ASP cc_start: 0.8456 (m-30) cc_final: 0.7270 (m-30) outliers start: 30 outliers final: 16 residues processed: 230 average time/residue: 0.2196 time to fit residues: 72.2933 Evaluate side-chains 195 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 239 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 29 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 55 optimal weight: 0.3980 chunk 59 optimal weight: 0.8980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN 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 = 0.3950 r_free = 0.3950 target = 0.127757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.084238 restraints weight = 20201.670| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.39 r_work: 0.3059 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 10450 Z= 0.277 Angle : 0.618 9.172 14149 Z= 0.313 Chirality : 0.042 0.149 1599 Planarity : 0.004 0.046 1761 Dihedral : 6.097 56.153 1728 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.49 % Allowed : 13.79 % Favored : 82.72 % 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: -0.17 (0.23), residues: 1272 helix: 1.44 (0.23), residues: 515 sheet: -1.12 (0.29), residues: 282 loop : -1.13 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 131 HIS 0.009 0.001 HIS E 232 PHE 0.015 0.001 PHE B 151 TYR 0.014 0.002 TYR E 190 ARG 0.006 0.000 ARG B 304 *********************** 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 210 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 172 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 26 MET cc_start: 0.6533 (OUTLIER) cc_final: 0.6113 (tpp) REVERT: R 56 TYR cc_start: 0.8089 (t80) cc_final: 0.7606 (t80) REVERT: R 65 ARG cc_start: 0.7578 (ttt180) cc_final: 0.6474 (mtm110) REVERT: R 130 ASP cc_start: 0.8855 (t70) cc_final: 0.8611 (t0) REVERT: R 132 TYR cc_start: 0.8313 (t80) cc_final: 0.8078 (t80) REVERT: R 207 TYR cc_start: 0.7843 (t80) cc_final: 0.7464 (t80) REVERT: R 276 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8498 (pt0) REVERT: R 283 PHE cc_start: 0.7823 (m-80) cc_final: 0.7510 (m-10) REVERT: R 292 SER cc_start: 0.9064 (m) cc_final: 0.8745 (p) REVERT: R 305 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7704 (tm-30) REVERT: R 313 CYS cc_start: 0.7446 (OUTLIER) cc_final: 0.6973 (p) REVERT: A 53 MET cc_start: 0.8428 (mtm) cc_final: 0.7958 (mtm) REVERT: A 224 CYS cc_start: 0.8980 (m) cc_final: 0.8337 (p) REVERT: A 330 LYS cc_start: 0.8723 (mmtt) cc_final: 0.8274 (ptmt) REVERT: B 7 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8640 (mm) REVERT: B 10 GLU cc_start: 0.9538 (tp30) cc_final: 0.9293 (tp30) REVERT: B 101 MET cc_start: 0.9330 (mtp) cc_final: 0.9044 (mtp) REVERT: B 209 LYS cc_start: 0.8994 (mttm) cc_final: 0.8697 (mttt) REVERT: B 243 THR cc_start: 0.9310 (m) cc_final: 0.9101 (p) REVERT: B 258 ASP cc_start: 0.8742 (t70) cc_final: 0.8473 (t0) REVERT: B 280 LYS cc_start: 0.9121 (mtpt) cc_final: 0.8900 (mtpp) REVERT: B 297 TRP cc_start: 0.9075 (m100) cc_final: 0.8294 (m100) REVERT: C 13 ARG cc_start: 0.9386 (mtt-85) cc_final: 0.8829 (ptp-110) REVERT: C 20 LYS cc_start: 0.9511 (ttpt) cc_final: 0.9128 (ptmm) REVERT: C 29 LYS cc_start: 0.8921 (mmmt) cc_final: 0.8680 (mmmt) REVERT: C 32 LYS cc_start: 0.9330 (tttt) cc_final: 0.8988 (tptp) REVERT: C 42 GLU cc_start: 0.8975 (tt0) cc_final: 0.8722 (tm-30) REVERT: C 58 GLU cc_start: 0.8751 (pt0) cc_final: 0.8128 (pm20) REVERT: E 45 LEU cc_start: 0.9108 (mt) cc_final: 0.8880 (mt) REVERT: E 51 ILE cc_start: 0.8449 (mp) cc_final: 0.8192 (mp) REVERT: E 73 ASP cc_start: 0.7932 (t70) cc_final: 0.6558 (t70) REVERT: E 93 MET cc_start: 0.8703 (ttm) cc_final: 0.8077 (tpt) REVERT: E 103 TYR cc_start: 0.8821 (t80) cc_final: 0.8606 (t80) REVERT: E 140 MET cc_start: 0.9115 (mmm) cc_final: 0.8122 (mmm) REVERT: E 210 THR cc_start: 0.8329 (m) cc_final: 0.8123 (p) REVERT: E 220 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8151 (mp0) REVERT: E 223 ASP cc_start: 0.8587 (m-30) cc_final: 0.6975 (m-30) outliers start: 38 outliers final: 22 residues processed: 198 average time/residue: 0.2168 time to fit residues: 61.3589 Evaluate side-chains 182 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 26 MET Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 267 HIS Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 293 MET Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 313 CYS Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 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 189 ILE 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: 2.9990 chunk 69 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 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 188 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 = 0.3917 r_free = 0.3917 target = 0.125488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.081992 restraints weight = 20009.972| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.32 r_work: 0.3022 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10450 Z= 0.276 Angle : 0.601 11.024 14149 Z= 0.305 Chirality : 0.043 0.147 1599 Planarity : 0.004 0.046 1761 Dihedral : 6.007 56.345 1728 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.94 % Allowed : 14.71 % Favored : 82.35 % 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: 0.04 (0.24), residues: 1272 helix: 1.60 (0.23), residues: 515 sheet: -0.93 (0.30), residues: 279 loop : -1.06 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.007 0.001 HIS E 232 PHE 0.015 0.001 PHE B 278 TYR 0.014 0.001 TYR E 190 ARG 0.006 0.000 ARG B 304 *********************** 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 206 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 1.181 Fit side-chains revert: symmetry clash REVERT: R 26 MET cc_start: 0.6486 (OUTLIER) cc_final: 0.5524 (tpt) REVERT: R 56 TYR cc_start: 0.8188 (t80) cc_final: 0.7646 (t80) REVERT: R 65 ARG cc_start: 0.7575 (ttt180) cc_final: 0.6487 (mtm110) REVERT: R 130 ASP cc_start: 0.8855 (t70) cc_final: 0.8609 (t0) REVERT: R 207 TYR cc_start: 0.7905 (t80) cc_final: 0.7421 (t80) REVERT: R 276 GLN cc_start: 0.8815 (mm-40) cc_final: 0.8434 (pt0) REVERT: R 283 PHE cc_start: 0.7879 (m-80) cc_final: 0.7667 (m-10) REVERT: R 292 SER cc_start: 0.9115 (m) cc_final: 0.8785 (p) REVERT: R 305 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7832 (tm-30) REVERT: R 313 CYS cc_start: 0.7526 (t) cc_final: 0.6969 (p) REVERT: A 224 CYS cc_start: 0.9042 (m) cc_final: 0.8291 (p) REVERT: A 330 LYS cc_start: 0.8773 (mmtt) cc_final: 0.8311 (ptmt) REVERT: B 10 GLU cc_start: 0.9520 (tp30) cc_final: 0.9312 (tp30) REVERT: B 101 MET cc_start: 0.9312 (mtp) cc_final: 0.9028 (mtp) REVERT: B 209 LYS cc_start: 0.8991 (mttm) cc_final: 0.8692 (mttt) REVERT: B 258 ASP cc_start: 0.8751 (t70) cc_final: 0.8407 (t0) REVERT: B 297 TRP cc_start: 0.9163 (m100) cc_final: 0.8216 (m100) REVERT: C 20 LYS cc_start: 0.9499 (ttpt) cc_final: 0.9094 (ptmm) REVERT: C 29 LYS cc_start: 0.8967 (mmmt) cc_final: 0.8740 (mmmt) REVERT: C 42 GLU cc_start: 0.9041 (tt0) cc_final: 0.8804 (tm-30) REVERT: C 58 GLU cc_start: 0.8777 (pt0) cc_final: 0.8174 (pm20) REVERT: E 73 ASP cc_start: 0.7758 (t70) cc_final: 0.7125 (t70) REVERT: E 93 MET cc_start: 0.8678 (ttm) cc_final: 0.8102 (tpt) REVERT: E 140 MET cc_start: 0.9189 (mmm) cc_final: 0.8648 (mmm) REVERT: E 210 THR cc_start: 0.8519 (m) cc_final: 0.8307 (p) REVERT: E 218 ARG cc_start: 0.8758 (ptp90) cc_final: 0.8403 (ptp90) REVERT: E 220 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8301 (mp0) REVERT: E 223 ASP cc_start: 0.8502 (m-30) cc_final: 0.7202 (m-30) outliers start: 32 outliers final: 21 residues processed: 195 average time/residue: 0.2132 time to fit residues: 59.5977 Evaluate side-chains 175 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 26 MET Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 312 HIS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 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: 5.9990 chunk 107 optimal weight: 0.9980 chunk 41 optimal weight: 30.0000 chunk 14 optimal weight: 9.9990 chunk 100 optimal weight: 0.0870 chunk 122 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 overall best weight: 1.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3915 r_free = 0.3915 target = 0.125709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.081399 restraints weight = 20018.235| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.37 r_work: 0.3006 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10450 Z= 0.258 Angle : 0.597 10.541 14149 Z= 0.302 Chirality : 0.042 0.171 1599 Planarity : 0.004 0.044 1761 Dihedral : 6.061 59.047 1728 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.03 % Allowed : 16.27 % Favored : 80.70 % 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 (0.24), residues: 1272 helix: 1.73 (0.23), residues: 515 sheet: -0.74 (0.30), residues: 273 loop : -1.06 (0.28), residues: 484 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 0.017 0.001 PHE B 278 TYR 0.013 0.001 TYR E 190 ARG 0.005 0.000 ARG B 304 *********************** 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 192 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: R 26 MET cc_start: 0.6590 (OUTLIER) cc_final: 0.5709 (tpt) REVERT: R 56 TYR cc_start: 0.8279 (t80) cc_final: 0.7647 (t80) REVERT: R 65 ARG cc_start: 0.7683 (ttt180) cc_final: 0.6563 (mtm110) REVERT: R 207 TYR cc_start: 0.7893 (t80) cc_final: 0.7329 (t80) REVERT: R 276 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8174 (pt0) REVERT: R 283 PHE cc_start: 0.7911 (m-80) cc_final: 0.7666 (m-10) REVERT: R 292 SER cc_start: 0.9236 (m) cc_final: 0.8891 (p) REVERT: R 305 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7678 (tm-30) REVERT: R 313 CYS cc_start: 0.7506 (t) cc_final: 0.6944 (p) REVERT: A 224 CYS cc_start: 0.8991 (m) cc_final: 0.8346 (p) REVERT: A 330 LYS cc_start: 0.8751 (mmtt) cc_final: 0.8293 (ptmt) REVERT: B 7 LEU cc_start: 0.8962 (mm) cc_final: 0.8751 (mm) REVERT: B 10 GLU cc_start: 0.9505 (tp30) cc_final: 0.9254 (tp30) REVERT: B 101 MET cc_start: 0.9294 (mtp) cc_final: 0.9035 (mtp) REVERT: B 209 LYS cc_start: 0.8952 (mttm) cc_final: 0.8644 (mttt) REVERT: B 258 ASP cc_start: 0.8627 (t70) cc_final: 0.8358 (t0) REVERT: B 262 MET cc_start: 0.8859 (mmp) cc_final: 0.8655 (mmp) REVERT: B 297 TRP cc_start: 0.9170 (m100) cc_final: 0.8240 (m100) REVERT: C 20 LYS cc_start: 0.9463 (ttpt) cc_final: 0.9079 (mtpp) REVERT: C 29 LYS cc_start: 0.8987 (mmmt) cc_final: 0.8651 (mmmt) REVERT: C 42 GLU cc_start: 0.9100 (tt0) cc_final: 0.8853 (tm-30) REVERT: C 58 GLU cc_start: 0.8802 (pt0) cc_final: 0.8176 (pm20) REVERT: E 51 ILE cc_start: 0.8329 (mp) cc_final: 0.8009 (mp) REVERT: E 73 ASP cc_start: 0.7869 (t70) cc_final: 0.7297 (t70) REVERT: E 93 MET cc_start: 0.8706 (ttm) cc_final: 0.8104 (tpt) REVERT: E 210 THR cc_start: 0.8658 (m) cc_final: 0.8447 (p) REVERT: E 218 ARG cc_start: 0.8808 (ptp90) cc_final: 0.8601 (ptp90) REVERT: E 220 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8416 (mm-30) REVERT: E 223 ASP cc_start: 0.8656 (m-30) cc_final: 0.8050 (m-30) outliers start: 33 outliers final: 24 residues processed: 179 average time/residue: 0.2231 time to fit residues: 56.8589 Evaluate side-chains 177 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 26 MET Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 267 HIS Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 312 HIS 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 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 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: 5.9990 chunk 34 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 109 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 ** 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 = 0.3892 r_free = 0.3892 target = 0.123959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.079842 restraints weight = 20102.916| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.30 r_work: 0.2973 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10450 Z= 0.289 Angle : 0.602 9.510 14149 Z= 0.306 Chirality : 0.042 0.156 1599 Planarity : 0.004 0.043 1761 Dihedral : 6.126 57.707 1728 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.58 % Allowed : 16.45 % Favored : 79.96 % 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: 0.23 (0.23), residues: 1272 helix: 1.79 (0.23), residues: 510 sheet: -0.61 (0.30), residues: 266 loop : -1.12 (0.27), residues: 496 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 0.017 0.001 PHE B 278 TYR 0.017 0.001 TYR R 70 ARG 0.005 0.000 ARG A 90 *********************** 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 194 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 1.414 Fit side-chains revert: symmetry clash REVERT: R 26 MET cc_start: 0.6747 (OUTLIER) cc_final: 0.5855 (tpt) REVERT: R 49 LEU cc_start: 0.8776 (mt) cc_final: 0.8517 (tp) REVERT: R 56 TYR cc_start: 0.8335 (t80) cc_final: 0.7857 (t80) REVERT: R 65 ARG cc_start: 0.7759 (ttt180) cc_final: 0.6622 (mtm110) REVERT: R 207 TYR cc_start: 0.7951 (t80) cc_final: 0.7404 (t80) REVERT: R 276 GLN cc_start: 0.8762 (mm-40) cc_final: 0.8089 (pt0) REVERT: R 283 PHE cc_start: 0.8042 (m-80) cc_final: 0.7791 (m-10) REVERT: R 292 SER cc_start: 0.9365 (m) cc_final: 0.9019 (p) REVERT: R 305 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7941 (tm-30) REVERT: R 313 CYS cc_start: 0.7514 (OUTLIER) cc_final: 0.6969 (p) REVERT: A 330 LYS cc_start: 0.8812 (mmtt) cc_final: 0.8396 (ptmt) REVERT: B 7 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8710 (mm) REVERT: B 10 GLU cc_start: 0.9492 (tp30) cc_final: 0.9235 (tp30) REVERT: B 101 MET cc_start: 0.9264 (mtp) cc_final: 0.8999 (mtp) REVERT: B 207 SER cc_start: 0.8870 (m) cc_final: 0.8326 (p) REVERT: B 209 LYS cc_start: 0.8988 (mttm) cc_final: 0.8775 (mttp) REVERT: B 258 ASP cc_start: 0.8597 (t70) cc_final: 0.8375 (t0) REVERT: C 20 LYS cc_start: 0.9460 (ttpt) cc_final: 0.9133 (mtpp) REVERT: C 58 GLU cc_start: 0.8842 (pt0) cc_final: 0.8171 (pm20) REVERT: E 73 ASP cc_start: 0.7966 (t70) cc_final: 0.7318 (t0) REVERT: E 83 MET cc_start: 0.8916 (mtm) cc_final: 0.8565 (mtm) REVERT: E 93 MET cc_start: 0.8766 (ttm) cc_final: 0.8085 (tpt) REVERT: E 218 ARG cc_start: 0.8813 (ptp90) cc_final: 0.8567 (ptp90) REVERT: E 220 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8355 (mm-30) REVERT: E 223 ASP cc_start: 0.8617 (m-30) cc_final: 0.8061 (m-30) outliers start: 39 outliers final: 23 residues processed: 182 average time/residue: 0.2532 time to fit residues: 65.1035 Evaluate side-chains 174 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 26 MET Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 267 HIS Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain 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 278 PHE Chi-restraints excluded: chain B residue 316 SER 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: 7.9990 chunk 64 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 33 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 75 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 = 0.3899 r_free = 0.3899 target = 0.124553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.081032 restraints weight = 20163.700| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 3.29 r_work: 0.3000 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10450 Z= 0.225 Angle : 0.584 8.556 14149 Z= 0.295 Chirality : 0.041 0.168 1599 Planarity : 0.004 0.054 1761 Dihedral : 6.053 57.641 1728 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.12 % Allowed : 17.00 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.37 (0.24), residues: 1272 helix: 1.90 (0.23), residues: 509 sheet: -0.57 (0.30), residues: 267 loop : -1.01 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS C 44 PHE 0.014 0.001 PHE B 278 TYR 0.014 0.001 TYR R 70 ARG 0.011 0.000 ARG A 90 *********************** 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 188 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: R 22 MET cc_start: 0.6414 (mmp) cc_final: 0.6105 (mmp) REVERT: R 26 MET cc_start: 0.6812 (OUTLIER) cc_final: 0.6183 (tpp) REVERT: R 49 LEU cc_start: 0.8775 (mt) cc_final: 0.8512 (tp) REVERT: R 56 TYR cc_start: 0.8353 (t80) cc_final: 0.7884 (t80) REVERT: R 65 ARG cc_start: 0.7673 (ttt180) cc_final: 0.6503 (mtm110) REVERT: R 207 TYR cc_start: 0.7938 (t80) cc_final: 0.7378 (t80) REVERT: R 276 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8571 (mm-40) REVERT: R 283 PHE cc_start: 0.7984 (m-80) cc_final: 0.7764 (m-10) REVERT: R 292 SER cc_start: 0.9327 (m) cc_final: 0.8974 (p) REVERT: R 305 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7974 (tm-30) REVERT: R 313 CYS cc_start: 0.7538 (OUTLIER) cc_final: 0.7077 (p) REVERT: A 193 ASP cc_start: 0.7839 (t0) cc_final: 0.7284 (t0) REVERT: A 330 LYS cc_start: 0.8799 (mmtt) cc_final: 0.8381 (ptmt) REVERT: B 7 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8684 (mm) REVERT: B 10 GLU cc_start: 0.9480 (tp30) cc_final: 0.9222 (tp30) REVERT: B 101 MET cc_start: 0.9211 (mtp) cc_final: 0.8966 (mtp) REVERT: B 207 SER cc_start: 0.8863 (m) cc_final: 0.8323 (p) REVERT: B 258 ASP cc_start: 0.8575 (t70) cc_final: 0.8371 (t0) REVERT: B 262 MET cc_start: 0.8930 (mmm) cc_final: 0.8662 (mmp) REVERT: B 280 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8792 (ttpt) REVERT: B 297 TRP cc_start: 0.9162 (m100) cc_final: 0.8311 (m100) REVERT: B 339 TRP cc_start: 0.9081 (m100) cc_final: 0.8606 (m100) REVERT: C 20 LYS cc_start: 0.9488 (ttpt) cc_final: 0.9168 (mtpp) REVERT: C 26 ASP cc_start: 0.8738 (p0) cc_final: 0.8509 (t0) REVERT: C 58 GLU cc_start: 0.8835 (pt0) cc_final: 0.8201 (pm20) REVERT: E 73 ASP cc_start: 0.7875 (t70) cc_final: 0.7247 (t0) REVERT: E 83 MET cc_start: 0.8905 (mtm) cc_final: 0.8546 (mtm) REVERT: E 93 MET cc_start: 0.8697 (ttm) cc_final: 0.8092 (tpt) REVERT: E 218 ARG cc_start: 0.8826 (ptp90) cc_final: 0.8560 (ptp90) REVERT: E 220 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8313 (mm-30) REVERT: E 223 ASP cc_start: 0.8597 (m-30) cc_final: 0.8014 (m-30) outliers start: 34 outliers final: 24 residues processed: 174 average time/residue: 0.2233 time to fit residues: 56.1177 Evaluate side-chains 181 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 26 MET Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 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 278 PHE Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 316 SER 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 233 LEU Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 0 optimal weight: 40.0000 chunk 56 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.121705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.077735 restraints weight = 20266.723| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.26 r_work: 0.2932 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10450 Z= 0.350 Angle : 0.639 7.652 14149 Z= 0.325 Chirality : 0.043 0.166 1599 Planarity : 0.004 0.042 1761 Dihedral : 6.468 59.488 1728 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.68 % Allowed : 16.18 % 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: 0.27 (0.23), residues: 1272 helix: 1.83 (0.23), residues: 507 sheet: -0.57 (0.31), residues: 261 loop : -1.11 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.004 0.001 HIS E 232 PHE 0.020 0.002 PHE B 278 TYR 0.013 0.002 TYR R 70 ARG 0.005 0.000 ARG E 98 *********************** 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 195 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 49 LEU cc_start: 0.8846 (mt) cc_final: 0.8597 (tp) REVERT: R 50 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8857 (mt-10) REVERT: R 65 ARG cc_start: 0.7756 (ttt180) cc_final: 0.6596 (mtm110) REVERT: R 207 TYR cc_start: 0.7993 (t80) cc_final: 0.7604 (t80) REVERT: R 276 GLN cc_start: 0.8911 (mm-40) cc_final: 0.8667 (mm-40) REVERT: R 292 SER cc_start: 0.9380 (m) cc_final: 0.8997 (p) REVERT: R 313 CYS cc_start: 0.7557 (OUTLIER) cc_final: 0.6926 (p) REVERT: A 330 LYS cc_start: 0.8866 (mmtt) cc_final: 0.8420 (ptmt) REVERT: B 7 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8708 (mm) REVERT: B 10 GLU cc_start: 0.9475 (tp30) cc_final: 0.9243 (tp30) REVERT: B 59 TYR cc_start: 0.9216 (m-80) cc_final: 0.8982 (m-80) REVERT: B 101 MET cc_start: 0.9246 (mtp) cc_final: 0.8966 (mtp) REVERT: B 207 SER cc_start: 0.8983 (m) cc_final: 0.8432 (p) REVERT: B 209 LYS cc_start: 0.8732 (mttp) cc_final: 0.8211 (mttt) REVERT: B 217 MET cc_start: 0.8679 (ppp) cc_final: 0.8170 (ppp) REVERT: B 262 MET cc_start: 0.8854 (mmm) cc_final: 0.8599 (mmp) REVERT: C 20 LYS cc_start: 0.9511 (ttpt) cc_final: 0.9189 (mtpp) REVERT: C 27 ARG cc_start: 0.8752 (mmt-90) cc_final: 0.8494 (mpt180) REVERT: C 29 LYS cc_start: 0.8753 (mmmt) cc_final: 0.8524 (mmmt) REVERT: C 58 GLU cc_start: 0.8869 (pt0) cc_final: 0.8182 (pm20) REVERT: E 73 ASP cc_start: 0.7998 (t70) cc_final: 0.7445 (t70) REVERT: E 83 MET cc_start: 0.8920 (mtm) cc_final: 0.8576 (mtm) REVERT: E 93 MET cc_start: 0.8852 (ttm) cc_final: 0.8103 (tpt) REVERT: E 140 MET cc_start: 0.9270 (mmm) cc_final: 0.9048 (mmm) REVERT: E 220 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8434 (mm-30) REVERT: E 223 ASP cc_start: 0.8589 (m-30) cc_final: 0.8010 (m-30) outliers start: 40 outliers final: 28 residues processed: 181 average time/residue: 0.2185 time to fit residues: 57.0507 Evaluate side-chains 175 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 CYS Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 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 321 THR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL 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: 0.4980 chunk 78 optimal weight: 4.9990 chunk 60 optimal weight: 0.0980 chunk 61 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 0.0170 chunk 30 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 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 = 0.3923 r_free = 0.3923 target = 0.126433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.083600 restraints weight = 20162.551| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.27 r_work: 0.3050 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10450 Z= 0.166 Angle : 0.595 8.472 14149 Z= 0.298 Chirality : 0.041 0.152 1599 Planarity : 0.003 0.040 1761 Dihedral : 6.115 58.697 1728 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.39 % Allowed : 17.56 % Favored : 80.06 % 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: 1.97 (0.22), residues: 510 sheet: -0.44 (0.31), residues: 277 loop : -1.05 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.004 0.001 HIS R 217 PHE 0.010 0.001 PHE A 189 TYR 0.014 0.001 TYR E 190 ARG 0.002 0.000 ARG E 98 *********************** 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 195 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 22 MET cc_start: 0.6598 (mmp) cc_final: 0.6254 (mmp) REVERT: R 49 LEU cc_start: 0.8820 (mt) cc_final: 0.8585 (tp) REVERT: R 65 ARG cc_start: 0.7731 (ttt180) cc_final: 0.6592 (mtm110) REVERT: R 207 TYR cc_start: 0.7906 (t80) cc_final: 0.7452 (t80) REVERT: R 239 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7391 (pp) REVERT: R 292 SER cc_start: 0.9304 (m) cc_final: 0.8957 (p) REVERT: R 313 CYS cc_start: 0.7430 (t) cc_final: 0.7021 (p) REVERT: A 193 ASP cc_start: 0.7843 (t0) cc_final: 0.7310 (t0) REVERT: A 330 LYS cc_start: 0.8802 (mmtt) cc_final: 0.8393 (ptmt) REVERT: B 7 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8696 (mm) REVERT: B 10 GLU cc_start: 0.9467 (tp30) cc_final: 0.9210 (tp30) REVERT: B 101 MET cc_start: 0.9061 (mtp) cc_final: 0.8805 (mtp) REVERT: B 207 SER cc_start: 0.9029 (m) cc_final: 0.8508 (p) REVERT: B 209 LYS cc_start: 0.8530 (mttp) cc_final: 0.8328 (mmtp) REVERT: B 217 MET cc_start: 0.8707 (ppp) cc_final: 0.8199 (ppp) REVERT: B 289 TYR cc_start: 0.8692 (m-80) cc_final: 0.8444 (m-80) REVERT: B 297 TRP cc_start: 0.9102 (m100) cc_final: 0.8466 (m100) REVERT: C 20 LYS cc_start: 0.9519 (ttpt) cc_final: 0.9189 (mtpp) REVERT: C 58 GLU cc_start: 0.8860 (pt0) cc_final: 0.8261 (pm20) REVERT: E 73 ASP cc_start: 0.7843 (t70) cc_final: 0.7231 (t0) REVERT: E 83 MET cc_start: 0.8873 (mtm) cc_final: 0.8505 (mtm) REVERT: E 93 MET cc_start: 0.8612 (ttm) cc_final: 0.8100 (tpt) REVERT: E 220 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8327 (mm-30) REVERT: E 223 ASP cc_start: 0.8443 (m-30) cc_final: 0.8013 (m-30) outliers start: 26 outliers final: 20 residues processed: 185 average time/residue: 0.2286 time to fit residues: 59.3155 Evaluate side-chains 178 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 267 HIS Chi-restraints excluded: chain R residue 312 HIS Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 82 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 29 optimal weight: 0.0970 chunk 95 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 276 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 = 0.3910 r_free = 0.3910 target = 0.125528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.082554 restraints weight = 20110.054| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 3.23 r_work: 0.3032 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10450 Z= 0.207 Angle : 0.632 9.494 14149 Z= 0.315 Chirality : 0.041 0.154 1599 Planarity : 0.004 0.060 1761 Dihedral : 6.104 60.363 1728 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.75 % Allowed : 18.75 % Favored : 79.50 % 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: 0.54 (0.24), residues: 1272 helix: 2.03 (0.23), residues: 509 sheet: -0.44 (0.30), residues: 283 loop : -0.93 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.004 0.001 HIS C 44 PHE 0.010 0.001 PHE A 189 TYR 0.015 0.001 TYR R 70 ARG 0.005 0.000 ARG A 90 ********************** 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 176 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 1.150 Fit side-chains revert: symmetry clash REVERT: R 22 MET cc_start: 0.6751 (mmp) cc_final: 0.6438 (mmp) REVERT: R 26 MET cc_start: 0.6833 (tpp) cc_final: 0.6615 (tpp) REVERT: R 49 LEU cc_start: 0.8840 (mt) cc_final: 0.8586 (tp) REVERT: R 65 ARG cc_start: 0.7763 (ttt180) cc_final: 0.6619 (mtm110) REVERT: R 207 TYR cc_start: 0.7937 (t80) cc_final: 0.7450 (t80) REVERT: R 292 SER cc_start: 0.9360 (m) cc_final: 0.9010 (p) REVERT: R 313 CYS cc_start: 0.7432 (t) cc_final: 0.7029 (p) REVERT: A 193 ASP cc_start: 0.7857 (t0) cc_final: 0.7316 (t0) REVERT: A 330 LYS cc_start: 0.8866 (mmtt) cc_final: 0.8421 (ptmt) REVERT: B 7 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8693 (mm) REVERT: B 10 GLU cc_start: 0.9463 (tp30) cc_final: 0.9202 (tp30) REVERT: B 16 ASN cc_start: 0.9342 (m110) cc_final: 0.9065 (p0) REVERT: B 101 MET cc_start: 0.9133 (mtp) cc_final: 0.8900 (mtp) REVERT: B 207 SER cc_start: 0.9005 (m) cc_final: 0.8501 (p) REVERT: B 209 LYS cc_start: 0.8540 (mttp) cc_final: 0.8001 (mttt) REVERT: B 262 MET cc_start: 0.8530 (mmm) cc_final: 0.8322 (mmm) REVERT: B 297 TRP cc_start: 0.9099 (m100) cc_final: 0.8355 (m100) REVERT: C 20 LYS cc_start: 0.9514 (ttpt) cc_final: 0.9182 (mtpp) REVERT: C 58 GLU cc_start: 0.8868 (pt0) cc_final: 0.8168 (pm20) REVERT: E 73 ASP cc_start: 0.7883 (t70) cc_final: 0.7267 (t0) REVERT: E 83 MET cc_start: 0.9002 (mtm) cc_final: 0.8693 (mtm) REVERT: E 93 MET cc_start: 0.8637 (ttm) cc_final: 0.8077 (tpt) REVERT: E 220 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8341 (mm-30) REVERT: E 223 ASP cc_start: 0.8483 (m-30) cc_final: 0.8015 (m-30) outliers start: 19 outliers final: 17 residues processed: 170 average time/residue: 0.2228 time to fit residues: 53.2064 Evaluate side-chains 170 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 267 HIS Chi-restraints excluded: chain R residue 312 HIS Chi-restraints excluded: chain A residue 321 THR 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 243 THR Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU 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: 0.0030 chunk 121 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 44 optimal weight: 30.0000 chunk 7 optimal weight: 20.0000 chunk 81 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 84 optimal weight: 4.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN ** 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 = 0.3899 r_free = 0.3899 target = 0.124802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.081372 restraints weight = 19964.388| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.25 r_work: 0.3012 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.5382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10450 Z= 0.241 Angle : 0.650 9.462 14149 Z= 0.325 Chirality : 0.042 0.147 1599 Planarity : 0.004 0.096 1761 Dihedral : 6.173 61.495 1728 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.48 % Allowed : 18.29 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.54 (0.24), residues: 1272 helix: 1.99 (0.22), residues: 509 sheet: -0.35 (0.31), residues: 266 loop : -0.94 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 339 HIS 0.004 0.001 HIS C 44 PHE 0.012 0.001 PHE B 278 TYR 0.016 0.001 TYR R 70 ARG 0.008 0.000 ARG A 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5912.44 seconds wall clock time: 105 minutes 37.83 seconds (6337.83 seconds total)