Starting phenix.real_space_refine on Thu Jul 2 16:04:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vuh_32128/07_2026/7vuh_32128.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vuh_32128/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7vuh_32128/07_2026/7vuh_32128.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vuh_32128/07_2026/7vuh_32128.cif" model { file = "/net/cci-nas-00/data/ceres_data/7vuh_32128/07_2026/7vuh_32128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vuh_32128/07_2026/7vuh_32128.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vuh_32128/07_2026/7vuh_32128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vuh_32128/07_2026/7vuh_32128.map" } 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-6108/lib/python3.11/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: 1.25, per 1000 atoms: 0.15 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 328.9 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: 0.14 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: 0.87 Time building geometry restraints manager: 0.71 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: 68 52.03 - 69.38: 8 69.38 - 86.72: 12 Dihedral angle restraints: 5040 sinusoidal: 1993 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 5037 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: 1.070 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: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.510 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 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 : 13.587 86.724 3064 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/Z covalent geometry : bond 0.00362 / 0.18 ( 8482) covalent geometry : angle 0.65588 / 0.36 (11502) SS BOND : bond 0.00333 / 0.17 ( 2) SS BOND : angle 1.61915 / 0.92 ( 4) hydrogen bonds : bond 0.17214 / 11.03 ( 365) hydrogen bonds : angle 7.46997 / 5.39 ( 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 : 0.235 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: 0.0818 time to fit residues: 23.0050 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 : 0.236 ------------------------------------------------------------------------------- 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... ** 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 = 0.3935 r_free = 0.3935 target = 0.158359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.142592 restraints weight = 11647.396| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.91 r_work: 0.3621 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.1289 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 : 0.647 7.872 11506 Z= 0.342 Chirality : 0.046 0.172 1299 Planarity : 0.005 0.056 1459 Dihedral : 5.165 48.196 1149 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 1.33 % Allowed : 10.53 % Favored : 88.14 % 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: -1.74 (0.26), residues: 1030 helix: 0.33 (0.28), residues: 384 sheet: -2.43 (0.32), residues: 186 loop : -1.84 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 379 TYR 0.022 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/Z covalent geometry : bond 0.00499 / 0.23 ( 8482) covalent geometry : angle 0.64539 / 0.34 (11502) SS BOND : bond 0.00598 / 0.31 ( 2) SS BOND : angle 2.60016 / 1.42 ( 4) hydrogen bonds : bond 0.04832 / 3.12 ( 365) hydrogen bonds : angle 5.75426 / 4.07 ( 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 227 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 215 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 221 MET cc_start: 0.8337 (ttp) cc_final: 0.8101 (ttp) REVERT: A 229 ASP cc_start: 0.7449 (p0) cc_final: 0.7200 (p0) REVERT: A 248 VAL cc_start: 0.8311 (p) cc_final: 0.8099 (t) REVERT: A 301 TYR cc_start: 0.7088 (m-80) cc_final: 0.6829 (t80) REVERT: A 313 ASP cc_start: 0.7499 (p0) cc_final: 0.7221 (p0) REVERT: A 330 PHE cc_start: 0.7669 (t80) cc_final: 0.7416 (t80) REVERT: A 360 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7588 (mm-30) REVERT: A 363 ARG cc_start: 0.7960 (tpp-160) cc_final: 0.7628 (tpp-160) REVERT: A 377 ASN cc_start: 0.8002 (m110) cc_final: 0.7572 (m-40) REVERT: B 43 ILE cc_start: 0.8500 (tp) cc_final: 0.8267 (pt) REVERT: B 84 SER cc_start: 0.7815 (OUTLIER) cc_final: 0.7517 (p) REVERT: B 301 LYS cc_start: 0.7630 (mttm) cc_final: 0.7358 (mttm) REVERT: G 58 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7738 (mm-30) REVERT: R 277 ASN cc_start: 0.7723 (t0) cc_final: 0.7517 (t0) REVERT: R 295 MET cc_start: 0.7437 (mmp) cc_final: 0.7150 (mmp) outliers start: 12 outliers final: 8 residues processed: 219 average time/residue: 0.0938 time to fit residues: 27.2540 Evaluate side-chains 209 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 200 time to evaluate : 0.179 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 17 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3948 r_free = 0.3948 target = 0.159176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.143442 restraints weight = 11720.241| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.86 r_work: 0.3638 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8484 Z= 0.171 Angle : 0.589 7.009 11506 Z= 0.312 Chirality : 0.044 0.155 1299 Planarity : 0.005 0.061 1459 Dihedral : 5.043 44.323 1149 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.00 % Allowed : 13.75 % Favored : 84.26 % 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: -1.56 (0.26), residues: 1030 helix: 0.46 (0.29), residues: 378 sheet: -2.14 (0.32), residues: 195 loop : -1.77 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 42 TYR 0.020 0.002 TYR N 80 PHE 0.015 0.002 PHE R 282 TRP 0.016 0.002 TRP A 234 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 8482) covalent geometry : angle 0.58829 / 0.31 (11502) SS BOND : bond 0.00313 / 0.16 ( 2) SS BOND : angle 2.02718 / 1.09 ( 4) hydrogen bonds : bond 0.04317 / 2.81 ( 365) hydrogen bonds : angle 5.43424 / 3.83 ( 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 226 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 208 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 229 ASP cc_start: 0.7446 (p0) cc_final: 0.7170 (p0) REVERT: A 248 VAL cc_start: 0.8298 (p) cc_final: 0.8039 (m) REVERT: A 301 TYR cc_start: 0.7025 (m-80) cc_final: 0.6786 (t80) REVERT: A 313 ASP cc_start: 0.7527 (p0) cc_final: 0.7251 (p0) REVERT: A 330 PHE cc_start: 0.7642 (t80) cc_final: 0.7386 (t80) REVERT: A 360 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7472 (mm-30) REVERT: A 363 ARG cc_start: 0.7982 (tpp-160) cc_final: 0.7642 (tpp-160) REVERT: A 377 ASN cc_start: 0.8013 (m110) cc_final: 0.7520 (m-40) REVERT: B 84 SER cc_start: 0.7791 (OUTLIER) cc_final: 0.7478 (p) REVERT: B 301 LYS cc_start: 0.7507 (mttm) cc_final: 0.7239 (mttm) REVERT: G 58 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7762 (mm-30) REVERT: R 117 TRP cc_start: 0.8102 (m100) cc_final: 0.7840 (m100) REVERT: R 295 MET cc_start: 0.7480 (mmp) cc_final: 0.7243 (mmp) outliers start: 18 outliers final: 10 residues processed: 215 average time/residue: 0.0928 time to fit residues: 26.4346 Evaluate side-chains 209 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 198 time to evaluate : 0.177 ------------------------------------------------------------------------------- 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 374 LEU 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: 0.6980 chunk 31 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 71 optimal weight: 0.4980 chunk 97 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 44 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 277 ASN 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 = 0.159493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.142843 restraints weight = 11801.255| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.96 r_work: 0.3637 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8484 Z= 0.166 Angle : 0.577 6.610 11506 Z= 0.305 Chirality : 0.043 0.155 1299 Planarity : 0.005 0.065 1459 Dihedral : 4.999 43.352 1149 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.55 % Allowed : 15.41 % 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: -1.49 (0.26), residues: 1030 helix: 0.56 (0.29), residues: 379 sheet: -1.96 (0.32), residues: 195 loop : -1.84 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 332 TYR 0.021 0.002 TYR N 80 PHE 0.016 0.001 PHE R 282 TRP 0.014 0.002 TRP B 82 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 ( 8482) covalent geometry : angle 0.57628 / 0.31 (11502) SS BOND : bond 0.00280 / 0.14 ( 2) SS BOND : angle 1.95422 / 1.05 ( 4) hydrogen bonds : bond 0.04134 / 2.71 ( 365) hydrogen bonds : angle 5.29021 / 3.72 ( 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 225 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 0.257 Fit side-chains REVERT: A 229 ASP cc_start: 0.7495 (p0) cc_final: 0.7241 (p0) REVERT: A 248 VAL cc_start: 0.8334 (p) cc_final: 0.8068 (t) REVERT: A 313 ASP cc_start: 0.7605 (p0) cc_final: 0.7319 (p0) REVERT: A 330 PHE cc_start: 0.7619 (t80) cc_final: 0.7413 (t80) REVERT: A 363 ARG cc_start: 0.7965 (tpp-160) cc_final: 0.7637 (tpp-160) REVERT: A 368 ASP cc_start: 0.7494 (m-30) cc_final: 0.7108 (t0) REVERT: B 55 LEU cc_start: 0.7755 (mt) cc_final: 0.7458 (mp) REVERT: B 301 LYS cc_start: 0.7487 (mttm) cc_final: 0.7213 (mttm) REVERT: G 58 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7776 (mm-30) REVERT: R 117 TRP cc_start: 0.8104 (m100) cc_final: 0.7837 (m100) REVERT: R 295 MET cc_start: 0.7460 (mmp) cc_final: 0.7224 (mmp) outliers start: 23 outliers final: 12 residues processed: 212 average time/residue: 0.0918 time to fit residues: 25.8055 Evaluate side-chains 210 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 198 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 359 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 187 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 24 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 5 optimal weight: 0.2980 chunk 71 optimal weight: 0.0060 chunk 54 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 44 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.157114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.140870 restraints weight = 11938.948| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.92 r_work: 0.3623 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.1860 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= 0.149 Angle : 0.569 6.366 11506 Z= 0.299 Chirality : 0.043 0.196 1299 Planarity : 0.005 0.065 1459 Dihedral : 4.949 43.061 1149 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.99 % Allowed : 16.63 % Favored : 80.38 % 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: -1.37 (0.26), residues: 1030 helix: 0.61 (0.28), residues: 379 sheet: -1.78 (0.33), residues: 195 loop : -1.80 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 332 TYR 0.021 0.001 TYR N 80 PHE 0.017 0.001 PHE R 282 TRP 0.014 0.002 TRP A 234 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 8482) covalent geometry : angle 0.56799 / 0.30 (11502) SS BOND : bond 0.00232 / 0.11 ( 2) SS BOND : angle 1.80402 / 0.97 ( 4) hydrogen bonds : bond 0.03982 / 2.60 ( 365) hydrogen bonds : angle 5.17083 / 3.64 ( 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 225 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 0.282 Fit side-chains REVERT: A 229 ASP cc_start: 0.7519 (p0) cc_final: 0.7266 (p0) REVERT: A 248 VAL cc_start: 0.8307 (p) cc_final: 0.8029 (t) REVERT: A 313 ASP cc_start: 0.7596 (p0) cc_final: 0.7299 (p0) REVERT: A 363 ARG cc_start: 0.7945 (tpp-160) cc_final: 0.7608 (tpp-160) REVERT: A 368 ASP cc_start: 0.7461 (m-30) cc_final: 0.7131 (t0) REVERT: B 55 LEU cc_start: 0.7795 (mt) cc_final: 0.7506 (mp) REVERT: B 84 SER cc_start: 0.7848 (OUTLIER) cc_final: 0.7450 (p) REVERT: B 292 PHE cc_start: 0.7557 (OUTLIER) cc_final: 0.7103 (m-80) REVERT: B 301 LYS cc_start: 0.7446 (mttm) cc_final: 0.7184 (mttm) REVERT: G 58 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7725 (mm-30) REVERT: R 117 TRP cc_start: 0.8069 (m100) cc_final: 0.7807 (m100) REVERT: R 295 MET cc_start: 0.7431 (mmp) cc_final: 0.7189 (mmp) outliers start: 27 outliers final: 14 residues processed: 213 average time/residue: 0.1024 time to fit residues: 28.8783 Evaluate side-chains 207 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 359 THR 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 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: 0.0570 chunk 72 optimal weight: 0.0670 chunk 45 optimal weight: 0.7980 chunk 34 optimal weight: 0.0980 chunk 71 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 60 optimal weight: 0.0070 overall best weight: 0.1654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.161482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.144917 restraints weight = 11702.249| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.01 r_work: 0.3647 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8484 Z= 0.108 Angle : 0.537 6.659 11506 Z= 0.282 Chirality : 0.042 0.150 1299 Planarity : 0.004 0.064 1459 Dihedral : 4.676 42.119 1149 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.10 % Allowed : 16.96 % Favored : 79.93 % 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: -1.14 (0.26), residues: 1030 helix: 0.72 (0.28), residues: 379 sheet: -1.52 (0.36), residues: 180 loop : -1.65 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 332 TYR 0.019 0.001 TYR N 80 PHE 0.031 0.001 PHE A 330 TRP 0.012 0.001 TRP A 234 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 ( 8482) covalent geometry : angle 0.53640 / 0.28 (11502) SS BOND : bond 0.00137 / 0.07 ( 2) SS BOND : angle 1.38665 / 0.74 ( 4) hydrogen bonds : bond 0.03643 / 2.40 ( 365) hydrogen bonds : angle 4.87005 / 3.42 ( 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 221 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.7790 (t) cc_final: 0.7554 (p) REVERT: A 229 ASP cc_start: 0.7535 (p0) cc_final: 0.7216 (p0) REVERT: A 248 VAL cc_start: 0.8333 (p) cc_final: 0.8018 (t) REVERT: A 313 ASP cc_start: 0.7601 (p0) cc_final: 0.7296 (p0) REVERT: A 360 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7467 (mm-30) REVERT: A 363 ARG cc_start: 0.7944 (tpp-160) cc_final: 0.7724 (tpp-160) REVERT: A 368 ASP cc_start: 0.7481 (m-30) cc_final: 0.7125 (t0) REVERT: B 55 LEU cc_start: 0.7727 (mt) cc_final: 0.7446 (mp) REVERT: B 301 LYS cc_start: 0.7412 (mttm) cc_final: 0.7188 (mttm) REVERT: R 295 MET cc_start: 0.7414 (mmp) cc_final: 0.7158 (mmp) outliers start: 28 outliers final: 17 residues processed: 212 average time/residue: 0.1091 time to fit residues: 30.8345 Evaluate side-chains 204 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 359 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 262 MET 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 149 ILE 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: 0.0670 chunk 79 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 95 optimal weight: 0.1980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 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 = 0.3963 r_free = 0.3963 target = 0.160354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.143545 restraints weight = 11893.386| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.05 r_work: 0.3615 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8484 Z= 0.144 Angle : 0.555 6.676 11506 Z= 0.294 Chirality : 0.043 0.150 1299 Planarity : 0.004 0.064 1459 Dihedral : 4.833 42.291 1149 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.33 % Allowed : 17.41 % 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: -1.13 (0.26), residues: 1030 helix: 0.70 (0.28), residues: 380 sheet: -1.44 (0.35), 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 0.020 0.001 TYR N 80 PHE 0.024 0.001 PHE A 330 TRP 0.013 0.001 TRP A 234 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 8482) covalent geometry : angle 0.55460 / 0.29 (11502) SS BOND : bond 0.00248 / 0.12 ( 2) SS BOND : angle 1.55681 / 0.84 ( 4) hydrogen bonds : bond 0.03857 / 2.52 ( 365) hydrogen bonds : angle 4.94389 / 3.48 ( 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 223 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.7785 (t) cc_final: 0.7545 (p) REVERT: A 229 ASP cc_start: 0.7591 (p0) cc_final: 0.7309 (p0) REVERT: A 248 VAL cc_start: 0.8338 (OUTLIER) cc_final: 0.8090 (t) REVERT: A 313 ASP cc_start: 0.7598 (p0) cc_final: 0.7291 (p0) REVERT: A 360 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7493 (mm-30) REVERT: A 363 ARG cc_start: 0.7963 (tpp-160) cc_final: 0.7630 (tpp-160) REVERT: B 55 LEU cc_start: 0.7770 (mt) cc_final: 0.7427 (mp) REVERT: B 76 ASP cc_start: 0.7370 (t0) cc_final: 0.7069 (t0) REVERT: B 292 PHE cc_start: 0.7625 (OUTLIER) cc_final: 0.7201 (m-80) REVERT: R 295 MET cc_start: 0.7419 (mmp) cc_final: 0.7176 (mmp) outliers start: 30 outliers final: 21 residues processed: 213 average time/residue: 0.0975 time to fit residues: 27.6616 Evaluate side-chains 218 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 195 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 248 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 146 LEU 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 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 149 ILE Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 281 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 58 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 56 optimal weight: 40.0000 chunk 77 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3924 r_free = 0.3924 target = 0.157369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.140427 restraints weight = 11862.008| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.07 r_work: 0.3610 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8484 Z= 0.178 Angle : 0.602 9.202 11506 Z= 0.313 Chirality : 0.044 0.159 1299 Planarity : 0.005 0.065 1459 Dihedral : 5.036 42.836 1149 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.33 % Allowed : 18.29 % Favored : 78.38 % 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: -1.13 (0.26), residues: 1030 helix: 0.68 (0.28), residues: 387 sheet: -1.46 (0.34), residues: 194 loop : -1.66 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 332 TYR 0.021 0.002 TYR N 80 PHE 0.021 0.002 PHE R 282 TRP 0.013 0.002 TRP A 234 HIS 0.004 0.001 HIS R 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 ( 8482) covalent geometry : angle 0.60092 / 0.31 (11502) SS BOND : bond 0.00315 / 0.16 ( 2) SS BOND : angle 2.08997 / 1.15 ( 4) hydrogen bonds : bond 0.04039 / 2.65 ( 365) hydrogen bonds : angle 5.08911 / 3.58 ( 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 225 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.7784 (t) cc_final: 0.7539 (p) REVERT: A 229 ASP cc_start: 0.7621 (p0) cc_final: 0.7343 (p0) REVERT: A 248 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.8068 (t) REVERT: A 313 ASP cc_start: 0.7641 (p0) cc_final: 0.7347 (p0) REVERT: A 363 ARG cc_start: 0.7991 (tpp-160) cc_final: 0.7643 (tpp-160) REVERT: A 368 ASP cc_start: 0.7531 (m-30) cc_final: 0.7159 (t0) REVERT: B 55 LEU cc_start: 0.7793 (mt) cc_final: 0.7445 (mp) REVERT: B 76 ASP cc_start: 0.7401 (t0) cc_final: 0.7101 (t0) REVERT: B 84 SER cc_start: 0.7802 (OUTLIER) cc_final: 0.7427 (p) REVERT: B 219 ARG cc_start: 0.7789 (mmt-90) cc_final: 0.7486 (mmt-90) REVERT: B 292 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.7261 (m-80) REVERT: B 301 LYS cc_start: 0.7605 (mttm) cc_final: 0.7384 (mttm) REVERT: N 109 ASP cc_start: 0.7724 (p0) cc_final: 0.7483 (p0) REVERT: R 295 MET cc_start: 0.7470 (mmp) cc_final: 0.7158 (mmp) outliers start: 30 outliers final: 21 residues processed: 218 average time/residue: 0.1033 time to fit residues: 29.9460 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 : 0.276 ------------------------------------------------------------------------------- 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 248 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 146 LEU 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 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 149 ILE Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 251 HIS Chi-restraints excluded: chain R residue 281 ASN 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: 0.8980 chunk 92 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 40 optimal weight: 0.0370 chunk 37 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN ** 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 = 0.3946 r_free = 0.3946 target = 0.159061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.142853 restraints weight = 11698.846| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 1.95 r_work: 0.3641 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8484 Z= 0.170 Angle : 0.589 6.584 11506 Z= 0.309 Chirality : 0.044 0.155 1299 Planarity : 0.005 0.066 1459 Dihedral : 5.065 43.853 1149 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.33 % Allowed : 18.40 % 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: -1.15 (0.26), residues: 1030 helix: 0.66 (0.28), residues: 385 sheet: -1.46 (0.34), residues: 196 loop : -1.66 (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 0.037 0.002 PHE A 330 TRP 0.013 0.002 TRP A 234 HIS 0.003 0.001 HIS R 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 8482) covalent geometry : angle 0.58773 / 0.31 (11502) SS BOND : bond 0.00350 / 0.18 ( 2) SS BOND : angle 2.08523 / 1.15 ( 4) hydrogen bonds : bond 0.04046 / 2.66 ( 365) hydrogen bonds : angle 5.08156 / 3.58 ( 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 226 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.287 Fit side-chains REVERT: A 36 VAL cc_start: 0.7770 (t) cc_final: 0.7531 (p) REVERT: A 49 ASP cc_start: 0.7366 (t0) cc_final: 0.6988 (t0) REVERT: A 229 ASP cc_start: 0.7616 (p0) cc_final: 0.7354 (p0) REVERT: A 248 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.8032 (t) REVERT: A 313 ASP cc_start: 0.7599 (p0) cc_final: 0.7290 (p0) REVERT: A 363 ARG cc_start: 0.7973 (tpp-160) cc_final: 0.7653 (tpp-160) REVERT: A 368 ASP cc_start: 0.7432 (m-30) cc_final: 0.7092 (t0) REVERT: B 55 LEU cc_start: 0.7759 (mt) cc_final: 0.7416 (mp) REVERT: B 76 ASP cc_start: 0.7349 (t0) cc_final: 0.7036 (t0) REVERT: B 84 SER cc_start: 0.7751 (OUTLIER) cc_final: 0.7396 (p) REVERT: B 292 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.7274 (m-80) REVERT: B 301 LYS cc_start: 0.7524 (mttm) cc_final: 0.7298 (mttm) REVERT: R 252 LEU cc_start: 0.7610 (tp) cc_final: 0.7361 (tt) REVERT: R 295 MET cc_start: 0.7416 (mmp) cc_final: 0.7104 (mmp) outliers start: 30 outliers final: 22 residues processed: 218 average time/residue: 0.1027 time to fit residues: 29.8803 Evaluate side-chains 220 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 239 ASN Chi-restraints excluded: chain A residue 248 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 146 LEU 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 281 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 36 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 91 optimal weight: 0.4980 chunk 75 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 4 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN ** 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 = 0.3928 r_free = 0.3928 target = 0.157592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.141002 restraints weight = 11790.150| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.05 r_work: 0.3612 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8484 Z= 0.165 Angle : 0.603 6.591 11506 Z= 0.318 Chirality : 0.044 0.156 1299 Planarity : 0.005 0.066 1459 Dihedral : 5.119 44.263 1149 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.55 % Allowed : 18.29 % Favored : 78.16 % 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: -1.15 (0.26), residues: 1030 helix: 0.59 (0.28), residues: 387 sheet: -1.46 (0.34), residues: 200 loop : -1.60 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 332 TYR 0.023 0.001 TYR N 80 PHE 0.044 0.002 PHE A 330 TRP 0.013 0.002 TRP A 234 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 ( 8482) covalent geometry : angle 0.60241 / 0.32 (11502) SS BOND : bond 0.00337 / 0.17 ( 2) SS BOND : angle 2.01643 / 1.11 ( 4) hydrogen bonds : bond 0.04112 / 2.73 ( 365) hydrogen bonds : angle 5.08301 / 3.58 ( 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 224 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.307 Fit side-chains REVERT: A 36 VAL cc_start: 0.7764 (t) cc_final: 0.7523 (p) REVERT: A 229 ASP cc_start: 0.7605 (p0) cc_final: 0.7322 (p0) REVERT: A 248 VAL cc_start: 0.8308 (OUTLIER) cc_final: 0.8014 (t) REVERT: A 249 ASP cc_start: 0.7670 (t0) cc_final: 0.7391 (t70) REVERT: A 313 ASP cc_start: 0.7590 (p0) cc_final: 0.7296 (p0) REVERT: A 360 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7502 (mm-30) REVERT: A 363 ARG cc_start: 0.7977 (tpp-160) cc_final: 0.7640 (tpp-160) REVERT: A 368 ASP cc_start: 0.7509 (m-30) cc_final: 0.7151 (t0) REVERT: B 55 LEU cc_start: 0.7770 (mt) cc_final: 0.7435 (mp) REVERT: B 76 ASP cc_start: 0.7410 (t0) cc_final: 0.7099 (t0) REVERT: B 84 SER cc_start: 0.7792 (OUTLIER) cc_final: 0.7425 (p) REVERT: B 212 ASP cc_start: 0.7260 (m-30) cc_final: 0.6861 (m-30) REVERT: B 292 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.7275 (m-80) REVERT: B 301 LYS cc_start: 0.7514 (mttm) cc_final: 0.7272 (mttm) REVERT: R 252 LEU cc_start: 0.7605 (tp) cc_final: 0.7355 (tt) REVERT: R 266 MET cc_start: 0.5350 (ptp) cc_final: 0.5145 (ppp) REVERT: R 295 MET cc_start: 0.7431 (mmp) cc_final: 0.7118 (mmp) outliers start: 32 outliers final: 26 residues processed: 216 average time/residue: 0.1064 time to fit residues: 30.6388 Evaluate side-chains 220 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 376 MET 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 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 N residue 96 CYS 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 149 ILE Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 281 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 ASN 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 = 0.3947 r_free = 0.3947 target = 0.159171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.143082 restraints weight = 11670.695| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.95 r_work: 0.3633 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 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 0.062 8484 Z= 0.195 Angle : 0.618 6.722 11506 Z= 0.324 Chirality : 0.045 0.163 1299 Planarity : 0.005 0.066 1459 Dihedral : 5.273 44.755 1149 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.44 % Allowed : 18.63 % 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: 0.64 (0.28), residues: 385 sheet: -1.49 (0.33), residues: 202 loop : -1.66 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 332 TYR 0.024 0.002 TYR N 80 PHE 0.038 0.002 PHE A 330 TRP 0.015 0.002 TRP A 271 HIS 0.004 0.001 HIS R 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 ( 8482) covalent geometry : angle 0.61664 / 0.32 (11502) SS BOND : bond 0.00338 / 0.17 ( 2) SS BOND : angle 2.08962 / 1.15 ( 4) hydrogen bonds : bond 0.04198 / 2.79 ( 365) hydrogen bonds : angle 5.11394 / 3.58 ( 1059) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2148.79 seconds wall clock time: 37 minutes 36.24 seconds (2256.24 seconds total)