Starting phenix.real_space_refine on Tue Mar 3 23:17:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vuh_32128/03_2026/7vuh_32128.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vuh_32128/03_2026/7vuh_32128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vuh_32128/03_2026/7vuh_32128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vuh_32128/03_2026/7vuh_32128.map" model { file = "/net/cci-nas-00/data/ceres_data/7vuh_32128/03_2026/7vuh_32128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vuh_32128/03_2026/7vuh_32128.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1050 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 50 5.16 5 Cl 1 4.86 5 C 5292 2.51 5 N 1436 2.21 5 O 1523 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8302 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1970 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2313 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 12, 'TRANS': 269} Chain: "R" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'7ZQ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.50, per 1000 atoms: 0.18 Number of scatterers: 8302 At special positions: 0 Unit cell: (76.96, 99.84, 134.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 50 16.00 O 1523 8.00 N 1436 7.00 C 5292 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 269.2 milliseconds 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1970 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 10 sheets defined 39.0% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 9 through 38 removed outlier: 3.734A pdb=" N ALA A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 removed outlier: 3.530A pdb=" N LEU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.675A pdb=" N ALA A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 292 removed outlier: 3.730A pdb=" N LEU A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 321 through 340 removed outlier: 3.649A pdb=" N ARG A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 381 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.540A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 74 through 77 removed outlier: 3.623A pdb=" N ASN N 77 " --> pdb=" O ASN N 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 74 through 77' Processing helix chain 'R' and resid 24 through 54 Proline residue: R 29 - end of helix Proline residue: R 42 - end of helix removed outlier: 3.843A pdb=" N GLN R 53 " --> pdb=" O ILE R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 59 removed outlier: 3.614A pdb=" N ARG R 58 " --> pdb=" O VAL R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 83 removed outlier: 4.149A pdb=" N ASN R 64 " --> pdb=" O LYS R 60 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL R 81 " --> pdb=" O LEU R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 91 Processing helix chain 'R' and resid 101 through 132 removed outlier: 3.594A pdb=" N LEU R 107 " --> pdb=" O ILE R 103 " (cutoff:3.500A) Proline residue: R 121 - end of helix Processing helix chain 'R' and resid 143 through 160 removed outlier: 3.645A pdb=" N VAL R 152 " --> pdb=" O VAL R 148 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR R 153 " --> pdb=" O ILE R 149 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE R 154 " --> pdb=" O VAL R 150 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR R 155 " --> pdb=" O SER R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 192 removed outlier: 3.715A pdb=" N HIS R 181 " --> pdb=" O THR R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 212 removed outlier: 4.003A pdb=" N LEU R 202 " --> pdb=" O ILE R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 254 removed outlier: 4.214A pdb=" N THR R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE R 237 " --> pdb=" O ILE R 233 " (cutoff:3.500A) Proline residue: R 243 - end of helix removed outlier: 3.955A pdb=" N LEU R 252 " --> pdb=" O ILE R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 261 removed outlier: 3.592A pdb=" N TRP R 261 " --> pdb=" O GLN R 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 258 through 261' Processing helix chain 'R' and resid 262 through 284 removed outlier: 4.148A pdb=" N MET R 266 " --> pdb=" O LEU R 262 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR R 278 " --> pdb=" O ALA R 274 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA R 279 " --> pdb=" O LEU R 275 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE R 282 " --> pdb=" O THR R 278 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE R 283 " --> pdb=" O ALA R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 289 through 300 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.617A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.719A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL A 277 " --> pdb=" O TYR A 350 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N HIS A 352 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU A 279 " --> pdb=" O HIS A 352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.547A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.853A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.461A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.505A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.174A 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 191 removed outlier: 3.554A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.415A 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: 3.533A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.360A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.570A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 59 through 60 removed outlier: 6.502A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 365 hydrogen bonds defined for protein. 1059 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.43 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1334 1.31 - 1.44: 2377 1.44 - 1.56: 4700 1.56 - 1.69: 0 1.69 - 1.82: 71 Bond restraints: 8482 Sorted by residual: bond pdb=" C9 7ZQ R 401 " pdb=" N2 7ZQ R 401 " ideal model delta sigma weight residual 1.341 1.447 -0.106 2.00e-02 2.50e+03 2.78e+01 bond pdb=" C7 7ZQ R 401 " pdb=" N1 7ZQ R 401 " ideal model delta sigma weight residual 1.344 1.448 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" C3 7ZQ R 401 " pdb="CL1 7ZQ R 401 " ideal model delta sigma weight residual 1.732 1.784 -0.052 2.00e-02 2.50e+03 6.72e+00 bond pdb=" C7 7ZQ R 401 " pdb=" O1 7ZQ R 401 " ideal model delta sigma weight residual 1.222 1.182 0.040 2.00e-02 2.50e+03 3.95e+00 bond pdb=" C9 7ZQ R 401 " pdb=" O2 7ZQ R 401 " ideal model delta sigma weight residual 1.219 1.180 0.039 2.00e-02 2.50e+03 3.77e+00 ... (remaining 8477 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 11129 1.56 - 3.12: 307 3.12 - 4.68: 43 4.68 - 6.24: 16 6.24 - 7.80: 7 Bond angle restraints: 11502 Sorted by residual: angle pdb=" N ILE R 118 " pdb=" CA ILE R 118 " pdb=" C ILE R 118 " ideal model delta sigma weight residual 111.81 107.53 4.28 8.60e-01 1.35e+00 2.47e+01 angle pdb=" C SER R 160 " pdb=" N ILE R 161 " pdb=" CA ILE R 161 " ideal model delta sigma weight residual 120.24 122.90 -2.66 6.30e-01 2.52e+00 1.79e+01 angle pdb=" C VAL R 191 " pdb=" N TYR R 192 " pdb=" CA TYR R 192 " ideal model delta sigma weight residual 122.17 116.39 5.78 1.54e+00 4.22e-01 1.41e+01 angle pdb=" C PHE R 27 " pdb=" N VAL R 28 " pdb=" CA VAL R 28 " ideal model delta sigma weight residual 120.24 122.30 -2.06 6.30e-01 2.52e+00 1.07e+01 angle pdb=" N GLY B 116 " pdb=" CA GLY B 116 " pdb=" C GLY B 116 " ideal model delta sigma weight residual 111.56 114.56 -3.00 1.01e+00 9.80e-01 8.84e+00 ... (remaining 11497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 4568 17.34 - 34.69: 384 34.69 - 52.03: 74 52.03 - 69.38: 8 69.38 - 86.72: 12 Dihedral angle restraints: 5046 sinusoidal: 1999 harmonic: 3047 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -29.67 -56.33 1 1.00e+01 1.00e-02 4.28e+01 dihedral pdb=" CA ASN R 168 " pdb=" C ASN R 168 " pdb=" N ILE R 169 " pdb=" CA ILE R 169 " ideal model delta harmonic sigma weight residual -180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA TRP R 117 " pdb=" C TRP R 117 " pdb=" N ILE R 118 " pdb=" CA ILE R 118 " ideal model delta harmonic sigma weight residual 180.00 160.69 19.31 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 5043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 798 0.033 - 0.065: 327 0.065 - 0.098: 115 0.098 - 0.130: 53 0.130 - 0.163: 6 Chirality restraints: 1299 Sorted by residual: chirality pdb=" CA LYS A 283 " pdb=" N LYS A 283 " pdb=" C LYS A 283 " pdb=" CB LYS A 283 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.64e-01 chirality pdb=" CB ILE R 104 " pdb=" CA ILE R 104 " pdb=" CG1 ILE R 104 " pdb=" CG2 ILE R 104 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.38e-01 chirality pdb=" CG LEU A 46 " pdb=" CB LEU A 46 " pdb=" CD1 LEU A 46 " pdb=" CD2 LEU A 46 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.65e-01 ... (remaining 1296 not shown) Planarity restraints: 1459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE R 82 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.33e+00 pdb=" C PHE R 82 " 0.040 2.00e-02 2.50e+03 pdb=" O PHE R 82 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL R 83 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR R 141 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO R 142 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO R 142 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 142 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 87 " -0.010 2.00e-02 2.50e+03 2.00e-02 4.00e+00 pdb=" C LEU R 87 " 0.035 2.00e-02 2.50e+03 pdb=" O LEU R 87 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU R 88 " -0.012 2.00e-02 2.50e+03 ... (remaining 1456 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 149 2.66 - 3.22: 8177 3.22 - 3.78: 13172 3.78 - 4.34: 18332 4.34 - 4.90: 29767 Nonbonded interactions: 69597 Sorted by model distance: nonbonded pdb=" OH TYR A 308 " pdb=" OD2 ASP A 333 " model vdw 2.099 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.131 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.137 3.040 nonbonded pdb=" OD1 ASP A 249 " pdb=" NZ LYS A 283 " model vdw 2.163 3.120 nonbonded pdb=" OD2 ASP B 27 " pdb=" OG SER G 31 " model vdw 2.197 3.040 ... (remaining 69592 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 8.570 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 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 : 0.004 0.106 8484 Z= 0.177 Angle : 0.656 7.796 11506 Z= 0.365 Chirality : 0.044 0.163 1299 Planarity : 0.004 0.051 1459 Dihedral : 13.682 86.724 3070 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.26), residues: 1030 helix: 0.32 (0.28), residues: 380 sheet: -2.64 (0.33), residues: 182 loop : -1.94 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 379 TYR 0.015 0.001 TYR R 253 PHE 0.020 0.002 PHE R 79 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8482) covalent geometry : angle 0.65588 (11502) SS BOND : bond 0.00333 ( 2) SS BOND : angle 1.61915 ( 4) hydrogen bonds : bond 0.17214 ( 365) hydrogen bonds : angle 7.46997 ( 1059) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.6520 (t0) cc_final: 0.6169 (t0) REVERT: A 248 VAL cc_start: 0.8214 (p) cc_final: 0.7980 (m) REVERT: A 313 ASP cc_start: 0.7203 (p0) cc_final: 0.6801 (p0) REVERT: A 368 ASP cc_start: 0.6576 (m-30) cc_final: 0.6062 (m-30) REVERT: A 377 ASN cc_start: 0.7683 (m110) cc_final: 0.7413 (m-40) REVERT: B 277 SER cc_start: 0.7898 (p) cc_final: 0.7624 (p) REVERT: G 58 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7160 (mm-30) REVERT: R 141 TYR cc_start: 0.7993 (p90) cc_final: 0.7621 (p90) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.1001 time to fit residues: 27.9349 Evaluate side-chains 201 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN R 181 HIS ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.158468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.142726 restraints weight = 11653.068| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.91 r_work: 0.3617 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 8484 Z= 0.225 Angle : 0.645 7.915 11506 Z= 0.342 Chirality : 0.046 0.171 1299 Planarity : 0.005 0.056 1459 Dihedral : 5.699 50.505 1155 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 1.44 % Allowed : 9.98 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.26), residues: 1030 helix: 0.33 (0.28), residues: 384 sheet: -2.41 (0.32), residues: 184 loop : -1.86 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 379 TYR 0.021 0.002 TYR R 253 PHE 0.017 0.002 PHE R 282 TRP 0.019 0.002 TRP A 234 HIS 0.006 0.001 HIS R 113 Details of bonding type rmsd covalent geometry : bond 0.00499 ( 8482) covalent geometry : angle 0.64388 (11502) SS BOND : bond 0.00573 ( 2) SS BOND : angle 2.52759 ( 4) hydrogen bonds : bond 0.04824 ( 365) hydrogen bonds : angle 5.76616 ( 1059) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 210 time to evaluate : 0.307 Fit side-chains REVERT: A 221 MET cc_start: 0.8347 (ttp) cc_final: 0.8112 (ttp) REVERT: A 229 ASP cc_start: 0.7459 (p0) cc_final: 0.7208 (p0) REVERT: A 301 TYR cc_start: 0.7097 (m-80) cc_final: 0.6839 (t80) REVERT: A 313 ASP cc_start: 0.7507 (p0) cc_final: 0.7227 (p0) REVERT: A 330 PHE cc_start: 0.7668 (t80) cc_final: 0.7416 (t80) REVERT: A 363 ARG cc_start: 0.7959 (tpp-160) cc_final: 0.7636 (tpp-160) REVERT: A 377 ASN cc_start: 0.8003 (m110) cc_final: 0.7568 (m-40) REVERT: B 43 ILE cc_start: 0.8501 (tp) cc_final: 0.8254 (pt) REVERT: B 84 SER cc_start: 0.7835 (OUTLIER) cc_final: 0.7532 (p) REVERT: B 301 LYS cc_start: 0.7626 (mttm) cc_final: 0.7355 (mttm) REVERT: G 58 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7766 (mm-30) REVERT: R 247 MET cc_start: 0.5524 (ttm) cc_final: 0.4102 (mtt) REVERT: R 266 MET cc_start: 0.5768 (ptp) cc_final: 0.5178 (ppp) REVERT: R 277 ASN cc_start: 0.7728 (t0) cc_final: 0.7522 (t0) REVERT: R 295 MET cc_start: 0.7473 (mmp) cc_final: 0.7209 (mmp) outliers start: 13 outliers final: 9 residues processed: 215 average time/residue: 0.1005 time to fit residues: 28.6430 Evaluate side-chains 207 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 197 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 123 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 14 optimal weight: 0.0980 chunk 17 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 68 optimal weight: 0.1980 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 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 = 0.3955 r_free = 0.3955 target = 0.159862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.143905 restraints weight = 11770.289| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.88 r_work: 0.3648 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8484 Z= 0.145 Angle : 0.562 6.640 11506 Z= 0.299 Chirality : 0.043 0.150 1299 Planarity : 0.005 0.062 1459 Dihedral : 5.340 45.602 1155 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.00 % Allowed : 14.08 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.26), residues: 1030 helix: 0.51 (0.29), residues: 377 sheet: -2.06 (0.32), residues: 195 loop : -1.70 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 231 TYR 0.021 0.001 TYR N 80 PHE 0.015 0.002 PHE R 282 TRP 0.015 0.002 TRP A 234 HIS 0.004 0.001 HIS R 113 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8482) covalent geometry : angle 0.56078 (11502) SS BOND : bond 0.00261 ( 2) SS BOND : angle 1.77913 ( 4) hydrogen bonds : bond 0.04120 ( 365) hydrogen bonds : angle 5.32536 ( 1059) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 205 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.7456 (p0) cc_final: 0.7153 (p0) REVERT: A 301 TYR cc_start: 0.7003 (m-80) cc_final: 0.6774 (t80) REVERT: A 313 ASP cc_start: 0.7521 (p0) cc_final: 0.7247 (p0) REVERT: A 330 PHE cc_start: 0.7617 (t80) cc_final: 0.7370 (t80) REVERT: A 360 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7454 (mm-30) REVERT: A 363 ARG cc_start: 0.7964 (tpp-160) cc_final: 0.7653 (tpp-160) REVERT: A 368 ASP cc_start: 0.7435 (m-30) cc_final: 0.7232 (m-30) REVERT: A 377 ASN cc_start: 0.8021 (m110) cc_final: 0.7528 (m-40) REVERT: B 34 THR cc_start: 0.6513 (p) cc_final: 0.6128 (p) REVERT: B 84 SER cc_start: 0.7758 (OUTLIER) cc_final: 0.7440 (p) REVERT: B 301 LYS cc_start: 0.7484 (mttm) cc_final: 0.7209 (mttm) REVERT: G 58 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7755 (mm-30) REVERT: R 117 TRP cc_start: 0.8077 (m100) cc_final: 0.7827 (m100) REVERT: R 295 MET cc_start: 0.7462 (mmp) cc_final: 0.7217 (mmp) outliers start: 18 outliers final: 9 residues processed: 211 average time/residue: 0.0985 time to fit residues: 27.0978 Evaluate side-chains 206 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 196 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 123 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 18 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 86 optimal weight: 0.3980 chunk 87 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 71 optimal weight: 0.2980 chunk 97 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 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 = 0.3935 r_free = 0.3935 target = 0.158095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.141300 restraints weight = 11926.743| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.07 r_work: 0.3617 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8484 Z= 0.152 Angle : 0.569 6.440 11506 Z= 0.300 Chirality : 0.043 0.203 1299 Planarity : 0.005 0.064 1459 Dihedral : 5.246 43.117 1155 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.33 % Allowed : 15.63 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.26), residues: 1030 helix: 0.62 (0.29), residues: 379 sheet: -1.89 (0.33), residues: 195 loop : -1.77 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 332 TYR 0.020 0.001 TYR N 80 PHE 0.016 0.001 PHE R 282 TRP 0.014 0.002 TRP A 234 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8482) covalent geometry : angle 0.56811 (11502) SS BOND : bond 0.00255 ( 2) SS BOND : angle 1.82101 ( 4) hydrogen bonds : bond 0.04060 ( 365) hydrogen bonds : angle 5.18554 ( 1059) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 207 time to evaluate : 0.233 Fit side-chains REVERT: A 42 ARG cc_start: 0.8077 (mtm-85) cc_final: 0.7849 (mtm-85) REVERT: A 229 ASP cc_start: 0.7511 (p0) cc_final: 0.7232 (p0) REVERT: A 301 TYR cc_start: 0.6921 (OUTLIER) cc_final: 0.6701 (t80) REVERT: A 313 ASP cc_start: 0.7601 (p0) cc_final: 0.7321 (p0) REVERT: A 330 PHE cc_start: 0.7628 (t80) cc_final: 0.7424 (t80) REVERT: A 360 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7554 (mm-30) REVERT: A 363 ARG cc_start: 0.7962 (tpp-160) cc_final: 0.7624 (tpp-160) REVERT: B 55 LEU cc_start: 0.7741 (mt) cc_final: 0.7437 (mp) REVERT: B 84 SER cc_start: 0.7779 (OUTLIER) cc_final: 0.7432 (p) REVERT: B 301 LYS cc_start: 0.7488 (mttm) cc_final: 0.7202 (mttm) REVERT: G 58 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7797 (mm-30) REVERT: R 117 TRP cc_start: 0.8102 (m100) cc_final: 0.7857 (m100) REVERT: R 161 ILE cc_start: 0.7883 (mm) cc_final: 0.7642 (mt) REVERT: R 295 MET cc_start: 0.7456 (mmp) cc_final: 0.7214 (mmp) outliers start: 21 outliers final: 11 residues processed: 218 average time/residue: 0.1006 time to fit residues: 28.8911 Evaluate side-chains 210 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 197 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 123 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 24 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 5 optimal weight: 0.2980 chunk 71 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 0.0870 chunk 59 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** R 277 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 = 0.3949 r_free = 0.3949 target = 0.159229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.142562 restraints weight = 11859.058| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.03 r_work: 0.3642 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8484 Z= 0.142 Angle : 0.558 6.393 11506 Z= 0.293 Chirality : 0.043 0.159 1299 Planarity : 0.004 0.065 1459 Dihedral : 5.137 42.511 1155 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.88 % Allowed : 16.96 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.26), residues: 1030 helix: 0.66 (0.29), residues: 378 sheet: -1.68 (0.34), residues: 195 loop : -1.74 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 332 TYR 0.020 0.001 TYR N 80 PHE 0.017 0.001 PHE R 282 TRP 0.013 0.001 TRP A 234 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8482) covalent geometry : angle 0.55686 (11502) SS BOND : bond 0.00211 ( 2) SS BOND : angle 1.65083 ( 4) hydrogen bonds : bond 0.03920 ( 365) hydrogen bonds : angle 5.09784 ( 1059) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 0.294 Fit side-chains REVERT: A 36 VAL cc_start: 0.7816 (t) cc_final: 0.7555 (p) REVERT: A 42 ARG cc_start: 0.8063 (mtm-85) cc_final: 0.7802 (mtm-85) REVERT: A 229 ASP cc_start: 0.7540 (p0) cc_final: 0.7277 (p0) REVERT: A 301 TYR cc_start: 0.6895 (OUTLIER) cc_final: 0.6669 (t80) REVERT: A 313 ASP cc_start: 0.7589 (p0) cc_final: 0.7279 (p0) REVERT: A 360 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7548 (mm-30) REVERT: A 363 ARG cc_start: 0.7991 (tpp-160) cc_final: 0.7669 (tpp-160) REVERT: A 368 ASP cc_start: 0.7468 (m-30) cc_final: 0.7116 (t0) REVERT: B 55 LEU cc_start: 0.7748 (mt) cc_final: 0.7466 (mp) REVERT: B 57 LYS cc_start: 0.8581 (ptpp) cc_final: 0.8355 (pttp) REVERT: B 84 SER cc_start: 0.7740 (OUTLIER) cc_final: 0.7376 (p) REVERT: B 292 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.7140 (m-80) REVERT: R 117 TRP cc_start: 0.8070 (m100) cc_final: 0.7835 (m100) REVERT: R 161 ILE cc_start: 0.7880 (mm) cc_final: 0.7633 (mt) REVERT: R 247 MET cc_start: 0.5482 (ttm) cc_final: 0.4641 (ttt) REVERT: R 266 MET cc_start: 0.5597 (ptp) cc_final: 0.5370 (ppp) REVERT: R 295 MET cc_start: 0.7432 (mmp) cc_final: 0.7188 (mmp) outliers start: 26 outliers final: 15 residues processed: 219 average time/residue: 0.1065 time to fit residues: 30.5627 Evaluate side-chains 220 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 281 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 44 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 277 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.157241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.140964 restraints weight = 11637.640| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.92 r_work: 0.3609 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 8484 Z= 0.245 Angle : 0.637 7.577 11506 Z= 0.337 Chirality : 0.046 0.174 1299 Planarity : 0.005 0.066 1459 Dihedral : 5.551 41.603 1155 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.55 % Allowed : 17.18 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.26), residues: 1030 helix: 0.48 (0.28), residues: 393 sheet: -1.76 (0.33), residues: 194 loop : -1.80 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 332 TYR 0.023 0.002 TYR N 80 PHE 0.029 0.002 PHE A 330 TRP 0.015 0.002 TRP A 234 HIS 0.005 0.001 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 8482) covalent geometry : angle 0.63572 (11502) SS BOND : bond 0.00311 ( 2) SS BOND : angle 2.10595 ( 4) hydrogen bonds : bond 0.04539 ( 365) hydrogen bonds : angle 5.39744 ( 1059) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 217 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.7798 (t) cc_final: 0.7480 (p) REVERT: A 301 TYR cc_start: 0.7145 (OUTLIER) cc_final: 0.6943 (t80) REVERT: A 313 ASP cc_start: 0.7608 (p0) cc_final: 0.7321 (p0) REVERT: A 368 ASP cc_start: 0.7434 (m-30) cc_final: 0.7083 (t0) REVERT: B 55 LEU cc_start: 0.7774 (mt) cc_final: 0.7481 (mp) REVERT: B 292 PHE cc_start: 0.7690 (OUTLIER) cc_final: 0.7289 (m-80) REVERT: N 109 ASP cc_start: 0.7864 (p0) cc_final: 0.7611 (p0) REVERT: R 117 TRP cc_start: 0.8163 (m100) cc_final: 0.7916 (m100) REVERT: R 161 ILE cc_start: 0.7909 (mm) cc_final: 0.7667 (mt) REVERT: R 273 LEU cc_start: 0.7625 (mt) cc_final: 0.7312 (mt) REVERT: R 295 MET cc_start: 0.7442 (mmp) cc_final: 0.7232 (mmp) outliers start: 32 outliers final: 21 residues processed: 236 average time/residue: 0.1028 time to fit residues: 32.3872 Evaluate side-chains 226 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 281 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 61 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 chunk 79 optimal weight: 0.5980 chunk 75 optimal weight: 0.0030 chunk 12 optimal weight: 0.2980 chunk 81 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 5 optimal weight: 0.0770 chunk 95 optimal weight: 0.8980 overall best weight: 0.2948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN R 251 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.160069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.143409 restraints weight = 11849.757| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.03 r_work: 0.3648 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8484 Z= 0.125 Angle : 0.566 6.664 11506 Z= 0.297 Chirality : 0.042 0.156 1299 Planarity : 0.005 0.067 1459 Dihedral : 5.153 43.381 1155 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.77 % Allowed : 18.29 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.26), residues: 1030 helix: 0.69 (0.28), residues: 380 sheet: -1.56 (0.34), residues: 193 loop : -1.68 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 332 TYR 0.022 0.001 TYR N 80 PHE 0.019 0.001 PHE A 330 TRP 0.012 0.002 TRP A 234 HIS 0.003 0.001 HIS R 251 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8482) covalent geometry : angle 0.56552 (11502) SS BOND : bond 0.00169 ( 2) SS BOND : angle 1.60658 ( 4) hydrogen bonds : bond 0.03848 ( 365) hydrogen bonds : angle 5.07565 ( 1059) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.7760 (t) cc_final: 0.7499 (p) REVERT: A 42 ARG cc_start: 0.8038 (mtm-85) cc_final: 0.7817 (mtm-85) REVERT: A 208 PHE cc_start: 0.7717 (m-10) cc_final: 0.7443 (m-80) REVERT: A 229 ASP cc_start: 0.7526 (p0) cc_final: 0.7318 (p0) REVERT: A 301 TYR cc_start: 0.6875 (OUTLIER) cc_final: 0.6647 (t80) REVERT: A 313 ASP cc_start: 0.7588 (p0) cc_final: 0.7287 (p0) REVERT: A 363 ARG cc_start: 0.7968 (tpp-160) cc_final: 0.7676 (tpp-160) REVERT: A 368 ASP cc_start: 0.7491 (m-30) cc_final: 0.7155 (t0) REVERT: B 55 LEU cc_start: 0.7735 (mt) cc_final: 0.7380 (mp) REVERT: B 76 ASP cc_start: 0.7343 (t0) cc_final: 0.7050 (t0) REVERT: B 84 SER cc_start: 0.7702 (OUTLIER) cc_final: 0.7319 (p) REVERT: B 292 PHE cc_start: 0.7634 (OUTLIER) cc_final: 0.7188 (m-80) REVERT: B 301 LYS cc_start: 0.7484 (mttm) cc_final: 0.7233 (mttm) REVERT: N 109 ASP cc_start: 0.7760 (p0) cc_final: 0.7522 (p0) REVERT: R 48 VAL cc_start: 0.6981 (t) cc_final: 0.6772 (p) REVERT: R 117 TRP cc_start: 0.8036 (m100) cc_final: 0.7758 (m100) REVERT: R 161 ILE cc_start: 0.7861 (mm) cc_final: 0.7614 (mt) REVERT: R 235 SER cc_start: 0.7532 (t) cc_final: 0.7273 (t) REVERT: R 295 MET cc_start: 0.7388 (mmp) cc_final: 0.7149 (mmp) outliers start: 34 outliers final: 21 residues processed: 223 average time/residue: 0.1051 time to fit residues: 30.7446 Evaluate side-chains 218 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 251 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 58 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 19 optimal weight: 0.0670 chunk 56 optimal weight: 0.0170 chunk 77 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 281 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.159846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.143171 restraints weight = 11744.118| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.03 r_work: 0.3644 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8484 Z= 0.138 Angle : 0.574 6.666 11506 Z= 0.300 Chirality : 0.043 0.140 1299 Planarity : 0.005 0.067 1459 Dihedral : 5.095 42.946 1155 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.10 % Allowed : 18.63 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.26), residues: 1030 helix: 0.73 (0.28), residues: 380 sheet: -1.45 (0.34), residues: 193 loop : -1.66 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 332 TYR 0.022 0.001 TYR N 80 PHE 0.017 0.001 PHE R 282 TRP 0.014 0.002 TRP B 99 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8482) covalent geometry : angle 0.57304 (11502) SS BOND : bond 0.00224 ( 2) SS BOND : angle 1.61663 ( 4) hydrogen bonds : bond 0.03836 ( 365) hydrogen bonds : angle 5.04388 ( 1059) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 0.277 Fit side-chains REVERT: A 36 VAL cc_start: 0.7756 (t) cc_final: 0.7511 (p) REVERT: A 42 ARG cc_start: 0.8065 (mtm-85) cc_final: 0.7826 (mtm-85) REVERT: A 208 PHE cc_start: 0.7764 (m-10) cc_final: 0.7457 (m-80) REVERT: A 229 ASP cc_start: 0.7581 (p0) cc_final: 0.7374 (p0) REVERT: A 301 TYR cc_start: 0.6966 (OUTLIER) cc_final: 0.6755 (t80) REVERT: A 313 ASP cc_start: 0.7589 (p0) cc_final: 0.7282 (p0) REVERT: A 363 ARG cc_start: 0.7963 (tpp-160) cc_final: 0.7634 (tpp-160) REVERT: A 368 ASP cc_start: 0.7478 (m-30) cc_final: 0.7118 (t0) REVERT: B 55 LEU cc_start: 0.7741 (mt) cc_final: 0.7426 (mp) REVERT: B 76 ASP cc_start: 0.7361 (t0) cc_final: 0.7056 (t0) REVERT: B 219 ARG cc_start: 0.7772 (mtt-85) cc_final: 0.7385 (mtt-85) REVERT: B 292 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.7227 (m-80) REVERT: B 301 LYS cc_start: 0.7541 (mttm) cc_final: 0.7301 (mttm) REVERT: N 109 ASP cc_start: 0.7851 (p0) cc_final: 0.7592 (p0) REVERT: R 117 TRP cc_start: 0.8040 (m100) cc_final: 0.7767 (m100) REVERT: R 148 VAL cc_start: 0.7233 (m) cc_final: 0.6936 (p) REVERT: R 161 ILE cc_start: 0.7859 (mm) cc_final: 0.7618 (mt) REVERT: R 295 MET cc_start: 0.7429 (mmp) cc_final: 0.7195 (mmp) outliers start: 28 outliers final: 22 residues processed: 218 average time/residue: 0.1008 time to fit residues: 29.2705 Evaluate side-chains 226 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 196 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 83 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 44 optimal weight: 0.0370 chunk 61 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 40 optimal weight: 0.0070 chunk 37 optimal weight: 0.8980 chunk 96 optimal weight: 0.0770 chunk 20 optimal weight: 0.7980 overall best weight: 0.2834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 340 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 = 0.3968 r_free = 0.3968 target = 0.161004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.144438 restraints weight = 11719.492| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.03 r_work: 0.3669 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8484 Z= 0.121 Angle : 0.557 7.006 11506 Z= 0.292 Chirality : 0.042 0.168 1299 Planarity : 0.004 0.066 1459 Dihedral : 4.963 43.159 1155 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.10 % Allowed : 19.07 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.26), residues: 1030 helix: 0.71 (0.28), residues: 380 sheet: -1.38 (0.34), residues: 195 loop : -1.61 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 332 TYR 0.022 0.001 TYR N 80 PHE 0.027 0.001 PHE A 330 TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8482) covalent geometry : angle 0.55591 (11502) SS BOND : bond 0.00253 ( 2) SS BOND : angle 2.00948 ( 4) hydrogen bonds : bond 0.03784 ( 365) hydrogen bonds : angle 4.98242 ( 1059) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 0.234 Fit side-chains REVERT: A 36 VAL cc_start: 0.7786 (t) cc_final: 0.7555 (p) REVERT: A 42 ARG cc_start: 0.8001 (mtm-85) cc_final: 0.7765 (mtm-85) REVERT: A 208 PHE cc_start: 0.7699 (m-10) cc_final: 0.7468 (m-80) REVERT: A 229 ASP cc_start: 0.7579 (p0) cc_final: 0.7348 (p0) REVERT: A 301 TYR cc_start: 0.6700 (OUTLIER) cc_final: 0.6491 (t80) REVERT: A 313 ASP cc_start: 0.7602 (p0) cc_final: 0.7314 (p0) REVERT: A 363 ARG cc_start: 0.7929 (tpp-160) cc_final: 0.7626 (tpp-160) REVERT: A 368 ASP cc_start: 0.7448 (m-30) cc_final: 0.7103 (t0) REVERT: B 55 LEU cc_start: 0.7726 (mt) cc_final: 0.7410 (mp) REVERT: B 76 ASP cc_start: 0.7309 (t0) cc_final: 0.6976 (t0) REVERT: B 219 ARG cc_start: 0.7698 (mtt-85) cc_final: 0.7318 (mtt-85) REVERT: B 292 PHE cc_start: 0.7621 (OUTLIER) cc_final: 0.7211 (m-80) REVERT: B 301 LYS cc_start: 0.7486 (mttm) cc_final: 0.7253 (mttm) REVERT: N 109 ASP cc_start: 0.7842 (p0) cc_final: 0.7546 (p0) REVERT: R 117 TRP cc_start: 0.7983 (m100) cc_final: 0.7758 (m100) REVERT: R 266 MET cc_start: 0.5490 (ptp) cc_final: 0.5206 (ppp) REVERT: R 295 MET cc_start: 0.7404 (mmp) cc_final: 0.7067 (mmp) outliers start: 28 outliers final: 20 residues processed: 216 average time/residue: 0.1009 time to fit residues: 28.7930 Evaluate side-chains 218 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 196 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 36 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 75 optimal weight: 0.1980 chunk 45 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 340 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 = 0.3951 r_free = 0.3951 target = 0.159585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.142999 restraints weight = 11678.463| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.01 r_work: 0.3632 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8484 Z= 0.157 Angle : 0.580 7.257 11506 Z= 0.305 Chirality : 0.043 0.165 1299 Planarity : 0.005 0.066 1459 Dihedral : 5.104 42.502 1155 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.55 % Allowed : 19.07 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.26), residues: 1030 helix: 0.62 (0.28), residues: 388 sheet: -1.38 (0.34), residues: 195 loop : -1.58 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 332 TYR 0.023 0.001 TYR N 80 PHE 0.027 0.002 PHE A 330 TRP 0.013 0.002 TRP A 234 HIS 0.003 0.001 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 8482) covalent geometry : angle 0.57839 (11502) SS BOND : bond 0.00336 ( 2) SS BOND : angle 2.07969 ( 4) hydrogen bonds : bond 0.03921 ( 365) hydrogen bonds : angle 5.07103 ( 1059) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 0.298 Fit side-chains REVERT: A 36 VAL cc_start: 0.7765 (t) cc_final: 0.7539 (p) REVERT: A 42 ARG cc_start: 0.8052 (mtm-85) cc_final: 0.7781 (mtm-85) REVERT: A 208 PHE cc_start: 0.7761 (m-10) cc_final: 0.7510 (m-80) REVERT: A 313 ASP cc_start: 0.7587 (p0) cc_final: 0.7268 (p0) REVERT: A 363 ARG cc_start: 0.7970 (tpp-160) cc_final: 0.7625 (tpp-160) REVERT: A 368 ASP cc_start: 0.7469 (m-30) cc_final: 0.7100 (t0) REVERT: B 55 LEU cc_start: 0.7743 (mt) cc_final: 0.7419 (mp) REVERT: B 76 ASP cc_start: 0.7334 (t0) cc_final: 0.7031 (t0) REVERT: B 219 ARG cc_start: 0.7728 (mtt-85) cc_final: 0.7350 (mtt-85) REVERT: B 292 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.7274 (m-80) REVERT: B 301 LYS cc_start: 0.7524 (mttm) cc_final: 0.7323 (mttm) REVERT: N 109 ASP cc_start: 0.7913 (p0) cc_final: 0.7633 (p0) REVERT: R 117 TRP cc_start: 0.8052 (m100) cc_final: 0.7794 (m100) REVERT: R 161 ILE cc_start: 0.7834 (mm) cc_final: 0.7594 (mt) REVERT: R 266 MET cc_start: 0.5529 (ptp) cc_final: 0.5296 (ppp) REVERT: R 295 MET cc_start: 0.7420 (mmp) cc_final: 0.7108 (mmp) outliers start: 32 outliers final: 24 residues processed: 217 average time/residue: 0.1063 time to fit residues: 30.2954 Evaluate side-chains 222 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 197 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 251 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 71 optimal weight: 0.0970 chunk 100 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN B 88 ASN B 230 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.159978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.143413 restraints weight = 11669.824| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.01 r_work: 0.3643 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8484 Z= 0.155 Angle : 0.583 9.445 11506 Z= 0.307 Chirality : 0.043 0.160 1299 Planarity : 0.005 0.066 1459 Dihedral : 5.136 43.602 1155 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.10 % Allowed : 20.07 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.26), residues: 1030 helix: 0.61 (0.28), residues: 388 sheet: -1.33 (0.35), residues: 193 loop : -1.52 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 332 TYR 0.023 0.001 TYR N 80 PHE 0.024 0.001 PHE R 282 TRP 0.014 0.002 TRP A 271 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 8482) covalent geometry : angle 0.58197 (11502) SS BOND : bond 0.00322 ( 2) SS BOND : angle 2.06011 ( 4) hydrogen bonds : bond 0.03949 ( 365) hydrogen bonds : angle 5.06054 ( 1059) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2243.82 seconds wall clock time: 39 minutes 8.43 seconds (2348.43 seconds total)