Starting phenix.real_space_refine on Thu Jul 2 09:37:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7f54_31457/07_2026/7f54_31457.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f54_31457/07_2026/7f54_31457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7f54_31457/07_2026/7f54_31457.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7f54_31457/07_2026/7f54_31457.cif" model { file = "/net/cci-nas-00/data/ceres_data/7f54_31457/07_2026/7f54_31457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f54_31457/07_2026/7f54_31457.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7f54_31457/07_2026/7f54_31457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f54_31457/07_2026/7f54_31457.map" } resolution = 3.0 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= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 62 5.16 5 C 5155 2.51 5 N 1403 2.21 5 O 1513 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 8134 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1885 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 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: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2133 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 7, 'TRANS': 265} Chain breaks: 2 Chain: "L" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 51 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'NLE:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 63 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DPN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1, 'water': 4} Link IDs: {None: 4} Time building chain proxies: 1.50, per 1000 atoms: 0.18 Number of scatterers: 8134 At special positions: 0 Unit cell: (86.19, 95.316, 122.694, 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) Ca 1 19.99 S 62 16.00 O 1513 8.00 N 1403 7.00 C 5155 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, 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 Simple disulfide: pdb=" SG CYS R 40 " - pdb=" SG CYS R 279 " distance=2.04 Simple disulfide: pdb=" SG CYS R 271 " - pdb=" SG CYS R 277 " distance=2.02 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 Links applied TRANS " DPN L 7 " - " HIS L 6 " Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 335.0 milliseconds 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DPN L 7 " Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 43.1% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.837A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.527A pdb=" N PHE A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.457A pdb=" N THR B 34 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN B 36 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.557A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 47 through 71 removed outlier: 3.827A pdb=" N PHE R 51 " --> pdb=" O SER R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 110 Processing helix chain 'R' and resid 117 through 153 Processing helix chain 'R' and resid 156 through 161 Processing helix chain 'R' and resid 162 through 187 Processing helix chain 'R' and resid 190 through 228 removed outlier: 3.919A pdb=" N ILE R 194 " --> pdb=" O SER R 190 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL R 228 " --> pdb=" O LYS R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 271 removed outlier: 3.734A pdb=" N PHE R 254 " --> pdb=" O LEU R 250 " (cutoff:3.500A) Proline residue: R 260 - end of helix Processing helix chain 'R' and resid 274 through 282 removed outlier: 3.621A pdb=" N CYS R 279 " --> pdb=" O PRO R 275 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 298 removed outlier: 3.920A pdb=" N ILE R 289 " --> pdb=" O ASN R 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 302 removed outlier: 3.629A pdb=" N TYR R 302 " --> pdb=" O PRO R 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 299 through 302' Processing helix chain 'R' and resid 306 through 320 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.305A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.909A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.632A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.010A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.845A 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 153 removed outlier: 3.524A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.680A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.120A 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: 6.103A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.750A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.553A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.506A pdb=" N GLY N 10 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA N 40 " --> pdb=" O GLY N 44 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY N 44 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1251 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: 1.01 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2627 1.34 - 1.46: 1919 1.46 - 1.58: 3651 1.58 - 1.71: 0 1.71 - 1.83: 87 Bond restraints: 8284 Sorted by residual: bond pdb=" C PHE A 273 " pdb=" O PHE A 273 " ideal model delta sigma weight residual 1.237 1.216 0.021 1.17e-02 7.31e+03 3.12e+00 bond pdb=" C ARG R 147 " pdb=" O ARG R 147 " ideal model delta sigma weight residual 1.237 1.216 0.021 1.17e-02 7.31e+03 3.10e+00 bond pdb=" C ALA R 144 " pdb=" O ALA R 144 " ideal model delta sigma weight residual 1.237 1.217 0.019 1.17e-02 7.31e+03 2.70e+00 bond pdb=" C LYS A 34 " pdb=" O LYS A 34 " ideal model delta sigma weight residual 1.237 1.218 0.018 1.17e-02 7.31e+03 2.44e+00 bond pdb=" C ALA R 70 " pdb=" N LYS R 71 " ideal model delta sigma weight residual 1.331 1.353 -0.023 1.48e-02 4.57e+03 2.36e+00 ... (remaining 8279 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 10648 1.87 - 3.75: 479 3.75 - 5.62: 70 5.62 - 7.50: 10 7.50 - 9.37: 3 Bond angle restraints: 11210 Sorted by residual: angle pdb=" N LYS B 78 " pdb=" CA LYS B 78 " pdb=" C LYS B 78 " ideal model delta sigma weight residual 108.69 117.01 -8.32 1.77e+00 3.19e-01 2.21e+01 angle pdb=" N LEU R 286 " pdb=" CA LEU R 286 " pdb=" C LEU R 286 " ideal model delta sigma weight residual 113.41 107.78 5.63 1.22e+00 6.72e-01 2.13e+01 angle pdb=" C ILE R 143 " pdb=" CA ILE R 143 " pdb=" CB ILE R 143 " ideal model delta sigma weight residual 111.97 106.80 5.17 1.28e+00 6.10e-01 1.63e+01 angle pdb=" N CYS N 96 " pdb=" CA CYS N 96 " pdb=" C CYS N 96 " ideal model delta sigma weight residual 109.76 103.42 6.34 1.64e+00 3.72e-01 1.49e+01 angle pdb=" N LYS R 71 " pdb=" CA LYS R 71 " pdb=" C LYS R 71 " ideal model delta sigma weight residual 113.16 117.67 -4.51 1.24e+00 6.50e-01 1.33e+01 ... (remaining 11205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 4656 17.58 - 35.16: 227 35.16 - 52.74: 49 52.74 - 70.32: 19 70.32 - 87.91: 5 Dihedral angle restraints: 4956 sinusoidal: 1949 harmonic: 3007 Sorted by residual: dihedral pdb=" CB CYS R 40 " pdb=" SG CYS R 40 " pdb=" SG CYS R 279 " pdb=" CB CYS R 279 " ideal model delta sinusoidal sigma weight residual -86.00 -35.53 -50.47 1 1.00e+01 1.00e-02 3.49e+01 dihedral pdb=" CA TRP R 258 " pdb=" C TRP R 258 " pdb=" N ALA R 259 " pdb=" CA ALA R 259 " ideal model delta harmonic sigma weight residual -180.00 -156.53 -23.47 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CB MET R 204 " pdb=" CG MET R 204 " pdb=" SD MET R 204 " pdb=" CE MET R 204 " ideal model delta sinusoidal sigma weight residual -180.00 -126.97 -53.03 3 1.50e+01 4.44e-03 9.17e+00 ... (remaining 4953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 967 0.055 - 0.111: 257 0.111 - 0.166: 46 0.166 - 0.222: 8 0.222 - 0.277: 2 Chirality restraints: 1280 Sorted by residual: chirality pdb=" CA TYR R 157 " pdb=" N TYR R 157 " pdb=" C TYR R 157 " pdb=" CB TYR R 157 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA HIS R 158 " pdb=" N HIS R 158 " pdb=" C HIS R 158 " pdb=" CB HIS R 158 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA GLU A 392 " pdb=" N GLU A 392 " pdb=" C GLU A 392 " pdb=" CB GLU A 392 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.64e-01 ... (remaining 1277 not shown) Planarity restraints: 1424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 382 " 0.021 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C ILE A 382 " -0.071 2.00e-02 2.50e+03 pdb=" O ILE A 382 " 0.027 2.00e-02 2.50e+03 pdb=" N ILE A 383 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 13 " 0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C ARG A 13 " -0.064 2.00e-02 2.50e+03 pdb=" O ARG A 13 " 0.024 2.00e-02 2.50e+03 pdb=" N ASN A 14 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 377 " -0.018 2.00e-02 2.50e+03 3.57e-02 1.27e+01 pdb=" C ASN A 377 " 0.062 2.00e-02 2.50e+03 pdb=" O ASN A 377 " -0.023 2.00e-02 2.50e+03 pdb=" N ASP A 378 " -0.021 2.00e-02 2.50e+03 ... (remaining 1421 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 678 2.74 - 3.28: 8125 3.28 - 3.82: 13191 3.82 - 4.36: 16492 4.36 - 4.90: 28408 Nonbonded interactions: 66894 Sorted by model distance: nonbonded pdb=" O ASP B 163 " pdb=" OD1 ASP B 163 " model vdw 2.194 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.216 3.040 nonbonded pdb=" OG SER R 58 " pdb=" OG SER R 94 " model vdw 2.244 3.040 nonbonded pdb=" OG SER R 116 " pdb=" N PHE R 117 " model vdw 2.259 3.120 nonbonded pdb=" OD2 ASP R 122 " pdb=" CG NLE L 4 " model vdw 2.302 3.440 ... (remaining 66889 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.480 Find NCS groups from input model: 0.040 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:5.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 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 0.039 8289 Z= 0.233 Angle : 0.895 9.374 11221 Z= 0.554 Chirality : 0.053 0.277 1280 Planarity : 0.006 0.041 1423 Dihedral : 11.935 87.906 2993 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.89 % Favored : 97.91 % Rotamer: Outliers : 0.22 % Allowed : 3.37 % Favored : 96.40 % 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: 1.16 (0.26), residues: 1006 helix: 0.98 (0.24), residues: 413 sheet: 0.79 (0.35), residues: 223 loop : 0.75 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG N 98 TYR 0.016 0.002 TYR A 339 PHE 0.025 0.003 PHE B 199 TRP 0.033 0.003 TRP B 99 HIS 0.008 0.002 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.23 ( 8284) covalent geometry : angle 0.89156 / 0.55 (11210) SS BOND : bond 0.00655 / 0.33 ( 4) SS BOND : angle 3.16046 / 1.28 ( 8) hydrogen bonds : bond 0.14710 / 9.89 ( 441) hydrogen bonds : angle 6.27302 / 4.45 ( 1251) link_TRANS : bond 0.00506 / 0.27 ( 1) link_TRANS : angle 0.63596 / 0.62 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 237 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7460 (tt0) cc_final: 0.7157 (tp-100) REVERT: A 293 LYS cc_start: 0.8370 (mttt) cc_final: 0.7754 (tmtt) REVERT: B 20 ASP cc_start: 0.6349 (m-30) cc_final: 0.5817 (p0) REVERT: B 265 SER cc_start: 0.7898 (p) cc_final: 0.7541 (m) REVERT: R 145 VAL cc_start: 0.7915 (OUTLIER) cc_final: 0.7668 (t) REVERT: R 204 MET cc_start: 0.6074 (mtt) cc_final: 0.5602 (mmt) outliers start: 2 outliers final: 1 residues processed: 239 average time/residue: 0.3660 time to fit residues: 93.5030 Evaluate side-chains 151 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 149 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 226 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 ASN B 176 GLN G 24 ASN R 72 ASN R 264 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.199538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.157291 restraints weight = 8699.790| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 2.62 r_work: 0.4010 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8289 Z= 0.137 Angle : 0.589 7.896 11221 Z= 0.320 Chirality : 0.042 0.150 1280 Planarity : 0.004 0.036 1423 Dihedral : 4.268 16.087 1124 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.48 % Allowed : 13.48 % Favored : 83.03 % 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: 2.01 (0.26), residues: 1006 helix: 2.18 (0.24), residues: 412 sheet: 1.23 (0.33), residues: 225 loop : 0.53 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 197 TYR 0.016 0.001 TYR B 85 PHE 0.017 0.002 PHE N 68 TRP 0.018 0.002 TRP B 169 HIS 0.009 0.001 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 ( 8284) covalent geometry : angle 0.58847 / 0.32 (11210) SS BOND : bond 0.00302 / 0.15 ( 4) SS BOND : angle 0.67912 / 0.32 ( 8) hydrogen bonds : bond 0.05055 / 3.33 ( 441) hydrogen bonds : angle 4.51528 / 3.19 ( 1251) link_TRANS : bond 0.00019 / 0.01 ( 1) link_TRANS : angle 0.40976 / 0.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7221 (OUTLIER) cc_final: 0.6931 (tp-100) REVERT: A 293 LYS cc_start: 0.8485 (mttt) cc_final: 0.7221 (tmtt) REVERT: A 343 ASP cc_start: 0.7890 (m-30) cc_final: 0.7401 (p0) REVERT: A 346 LEU cc_start: 0.7405 (mt) cc_final: 0.7130 (mt) REVERT: A 364 THR cc_start: 0.6785 (p) cc_final: 0.6459 (t) REVERT: A 374 ARG cc_start: 0.8190 (mtt180) cc_final: 0.7964 (mtm-85) REVERT: B 20 ASP cc_start: 0.6726 (m-30) cc_final: 0.6026 (p0) REVERT: B 186 ASP cc_start: 0.5740 (OUTLIER) cc_final: 0.5438 (m-30) REVERT: B 217 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.7095 (ptm) REVERT: B 234 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.7256 (OUTLIER) REVERT: B 251 ARG cc_start: 0.7196 (mtm-85) cc_final: 0.6966 (mtm-85) REVERT: B 280 LYS cc_start: 0.8219 (tttt) cc_final: 0.7890 (tttt) REVERT: B 325 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.8035 (tpp) REVERT: G 44 HIS cc_start: 0.5860 (m170) cc_final: 0.5180 (t-170) REVERT: N 77 ASN cc_start: 0.7755 (m-40) cc_final: 0.7517 (t0) outliers start: 31 outliers final: 11 residues processed: 187 average time/residue: 0.3674 time to fit residues: 73.8230 Evaluate side-chains 147 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 226 ILE Chi-restraints excluded: chain R residue 312 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 90 optimal weight: 0.0070 chunk 38 optimal weight: 6.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 ASN A 387 HIS A 390 GLN B 259 GLN G 24 ASN R 72 ASN R 76 HIS R 264 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.192904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.150717 restraints weight = 8753.756| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 2.59 r_work: 0.3892 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8289 Z= 0.172 Angle : 0.587 7.264 11221 Z= 0.321 Chirality : 0.043 0.154 1280 Planarity : 0.004 0.034 1423 Dihedral : 4.491 19.387 1123 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.61 % Allowed : 14.83 % Favored : 80.56 % 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: 1.78 (0.26), residues: 1006 helix: 2.19 (0.25), residues: 412 sheet: 1.10 (0.32), residues: 220 loop : 0.14 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 380 TYR 0.015 0.002 TYR N 95 PHE 0.030 0.002 PHE B 241 TRP 0.020 0.002 TRP B 169 HIS 0.012 0.002 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 ( 8284) covalent geometry : angle 0.58745 / 0.32 (11210) SS BOND : bond 0.00325 / 0.16 ( 4) SS BOND : angle 0.71677 / 0.44 ( 8) hydrogen bonds : bond 0.05171 / 3.45 ( 441) hydrogen bonds : angle 4.45208 / 3.17 ( 1251) link_TRANS : bond 0.00073 / 0.04 ( 1) link_TRANS : angle 0.31537 / 0.28 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 148 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6790 (tppt) REVERT: A 35 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6701 (tm-30) REVERT: A 293 LYS cc_start: 0.8430 (mttt) cc_final: 0.7048 (tmtt) REVERT: A 339 TYR cc_start: 0.7732 (m-80) cc_final: 0.7508 (m-80) REVERT: A 342 ARG cc_start: 0.7004 (ttp-170) cc_final: 0.6284 (ttm-80) REVERT: A 346 LEU cc_start: 0.7573 (mt) cc_final: 0.7303 (mt) REVERT: A 364 THR cc_start: 0.6988 (p) cc_final: 0.6703 (t) REVERT: A 374 ARG cc_start: 0.8317 (mtt180) cc_final: 0.8029 (mtm-85) REVERT: B 20 ASP cc_start: 0.6753 (m-30) cc_final: 0.6189 (p0) REVERT: B 175 GLN cc_start: 0.6914 (tp40) cc_final: 0.6538 (mm-40) REVERT: B 186 ASP cc_start: 0.5907 (OUTLIER) cc_final: 0.5654 (m-30) REVERT: B 217 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7240 (ptm) REVERT: B 234 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7503 (OUTLIER) REVERT: B 325 MET cc_start: 0.8486 (mmt) cc_final: 0.8286 (tpp) REVERT: G 44 HIS cc_start: 0.6199 (m170) cc_final: 0.5574 (t-170) REVERT: R 51 PHE cc_start: 0.6549 (OUTLIER) cc_final: 0.6262 (m-80) REVERT: R 292 MET cc_start: 0.6250 (mtp) cc_final: 0.5857 (mtt) outliers start: 41 outliers final: 12 residues processed: 171 average time/residue: 0.3338 time to fit residues: 61.5067 Evaluate side-chains 141 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain R residue 51 PHE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 296 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 24 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 59 optimal weight: 0.0010 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 236 GLN R 264 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.192375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.149306 restraints weight = 8935.613| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 2.70 r_work: 0.3913 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8289 Z= 0.130 Angle : 0.551 9.434 11221 Z= 0.293 Chirality : 0.042 0.139 1280 Planarity : 0.004 0.040 1423 Dihedral : 4.262 18.671 1121 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.37 % Allowed : 17.75 % Favored : 78.88 % 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: 1.83 (0.26), residues: 1006 helix: 2.36 (0.25), residues: 406 sheet: 1.10 (0.34), residues: 205 loop : 0.11 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 98 TYR 0.013 0.001 TYR N 95 PHE 0.017 0.002 PHE A 376 TRP 0.017 0.002 TRP B 169 HIS 0.011 0.001 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 8284) covalent geometry : angle 0.55111 / 0.29 (11210) SS BOND : bond 0.00277 / 0.14 ( 4) SS BOND : angle 0.51248 / 0.25 ( 8) hydrogen bonds : bond 0.04543 / 3.02 ( 441) hydrogen bonds : angle 4.22400 / 2.99 ( 1251) link_TRANS : bond 0.00043 / 0.02 ( 1) link_TRANS : angle 0.40014 / 0.37 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.6897 (tppt) REVERT: A 35 GLN cc_start: 0.7238 (OUTLIER) cc_final: 0.7033 (tp-100) REVERT: A 267 GLN cc_start: 0.7882 (tp40) cc_final: 0.7418 (tm-30) REVERT: A 293 LYS cc_start: 0.8332 (mttt) cc_final: 0.6982 (tmtt) REVERT: A 339 TYR cc_start: 0.7718 (m-80) cc_final: 0.7468 (m-80) REVERT: A 346 LEU cc_start: 0.7601 (mt) cc_final: 0.7333 (mt) REVERT: A 364 THR cc_start: 0.6974 (p) cc_final: 0.6658 (t) REVERT: B 175 GLN cc_start: 0.6989 (tp40) cc_final: 0.6695 (mm-40) REVERT: B 217 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.7299 (ptm) REVERT: B 325 MET cc_start: 0.8358 (mmt) cc_final: 0.8053 (tpp) REVERT: B 336 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8073 (mt) REVERT: G 16 VAL cc_start: 0.7124 (m) cc_final: 0.6863 (t) REVERT: G 44 HIS cc_start: 0.6304 (m170) cc_final: 0.5709 (t-170) REVERT: N 38 ARG cc_start: 0.7035 (ttm170) cc_final: 0.6576 (ttm170) REVERT: N 46 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6588 (mm-30) REVERT: R 297 ILE cc_start: 0.7091 (OUTLIER) cc_final: 0.6511 (tp) outliers start: 30 outliers final: 12 residues processed: 163 average time/residue: 0.3361 time to fit residues: 58.8231 Evaluate side-chains 139 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 296 ILE Chi-restraints excluded: chain R residue 297 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 45 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 HIS A 236 GLN ** R 264 HIS ** 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 = 0.4436 r_free = 0.4436 target = 0.187834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.145264 restraints weight = 8937.327| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.69 r_work: 0.3832 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 8289 Z= 0.202 Angle : 0.648 11.099 11221 Z= 0.345 Chirality : 0.045 0.168 1280 Planarity : 0.004 0.038 1423 Dihedral : 4.585 17.099 1121 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.61 % Allowed : 19.21 % Favored : 76.18 % 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: 1.42 (0.26), residues: 1006 helix: 2.03 (0.25), residues: 412 sheet: 0.85 (0.35), residues: 193 loop : -0.10 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 283 TYR 0.019 0.002 TYR N 95 PHE 0.023 0.002 PHE B 335 TRP 0.021 0.003 TRP R 258 HIS 0.013 0.002 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 ( 8284) covalent geometry : angle 0.64775 / 0.34 (11210) SS BOND : bond 0.00346 / 0.17 ( 4) SS BOND : angle 0.76297 / 0.36 ( 8) hydrogen bonds : bond 0.05270 / 3.52 ( 441) hydrogen bonds : angle 4.51699 / 3.21 ( 1251) link_TRANS : bond 0.00141 / 0.07 ( 1) link_TRANS : angle 0.43764 / 0.42 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6579 (tppp) REVERT: A 35 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.6616 (tm-30) REVERT: A 236 GLN cc_start: 0.8220 (mt0) cc_final: 0.7987 (mt0) REVERT: A 293 LYS cc_start: 0.8254 (mttt) cc_final: 0.6856 (tmtt) REVERT: A 339 TYR cc_start: 0.7787 (m-80) cc_final: 0.7490 (m-80) REVERT: A 342 ARG cc_start: 0.6954 (ttp-170) cc_final: 0.6197 (ttm-80) REVERT: A 346 LEU cc_start: 0.7682 (mt) cc_final: 0.7327 (mt) REVERT: B 16 ASN cc_start: 0.7815 (m-40) cc_final: 0.6840 (t160) REVERT: B 98 SER cc_start: 0.8830 (OUTLIER) cc_final: 0.8326 (t) REVERT: B 127 LYS cc_start: 0.6445 (mttt) cc_final: 0.6244 (mttt) REVERT: B 175 GLN cc_start: 0.7349 (tp40) cc_final: 0.6952 (mm-40) REVERT: B 217 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.7323 (ptm) REVERT: B 226 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7403 (mt-10) REVERT: B 239 ASN cc_start: 0.7250 (m110) cc_final: 0.6379 (t0) REVERT: B 325 MET cc_start: 0.8624 (mmt) cc_final: 0.8299 (tpp) REVERT: B 336 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8079 (mt) REVERT: G 44 HIS cc_start: 0.6585 (m170) cc_final: 0.5807 (t-170) REVERT: R 273 GLN cc_start: 0.7148 (OUTLIER) cc_final: 0.6782 (mp10) REVERT: R 281 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7746 (mpt) REVERT: R 297 ILE cc_start: 0.7233 (OUTLIER) cc_final: 0.6793 (tp) outliers start: 41 outliers final: 18 residues processed: 159 average time/residue: 0.3672 time to fit residues: 62.6720 Evaluate side-chains 147 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 273 GLN Chi-restraints excluded: chain R residue 281 MET Chi-restraints excluded: chain R residue 296 ILE Chi-restraints excluded: chain R residue 297 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 30 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 ASN R 264 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.194172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.152120 restraints weight = 8755.100| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 2.60 r_work: 0.3901 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8289 Z= 0.131 Angle : 0.591 12.377 11221 Z= 0.308 Chirality : 0.042 0.140 1280 Planarity : 0.004 0.042 1423 Dihedral : 4.314 17.014 1121 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.71 % Allowed : 21.57 % Favored : 74.72 % 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: 1.64 (0.26), residues: 1006 helix: 2.32 (0.25), residues: 406 sheet: 0.92 (0.35), residues: 192 loop : -0.04 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 380 TYR 0.017 0.001 TYR A 358 PHE 0.014 0.001 PHE B 199 TRP 0.017 0.002 TRP B 169 HIS 0.012 0.001 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 8284) covalent geometry : angle 0.59116 / 0.31 (11210) SS BOND : bond 0.00249 / 0.12 ( 4) SS BOND : angle 0.51349 / 0.26 ( 8) hydrogen bonds : bond 0.04444 / 2.97 ( 441) hydrogen bonds : angle 4.26340 / 3.02 ( 1251) link_TRANS : bond 0.00013 / 0.01 ( 1) link_TRANS : angle 0.38672 / 0.35 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7197 (OUTLIER) cc_final: 0.6635 (tppp) REVERT: A 35 GLN cc_start: 0.7150 (OUTLIER) cc_final: 0.6703 (tm-30) REVERT: A 293 LYS cc_start: 0.8245 (mttt) cc_final: 0.6862 (tmtt) REVERT: A 339 TYR cc_start: 0.7716 (m-80) cc_final: 0.7462 (m-80) REVERT: A 342 ARG cc_start: 0.6894 (ttp-170) cc_final: 0.6196 (ttm-80) REVERT: B 16 ASN cc_start: 0.7743 (m-40) cc_final: 0.6787 (t160) REVERT: B 175 GLN cc_start: 0.7259 (tp40) cc_final: 0.6892 (mm-40) REVERT: B 186 ASP cc_start: 0.5527 (OUTLIER) cc_final: 0.5326 (m-30) REVERT: B 217 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7312 (ptm) REVERT: B 239 ASN cc_start: 0.7135 (m110) cc_final: 0.6355 (t0) REVERT: B 325 MET cc_start: 0.8561 (mmt) cc_final: 0.8269 (tpp) REVERT: B 336 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7994 (mt) REVERT: G 44 HIS cc_start: 0.6461 (m170) cc_final: 0.5881 (t-170) REVERT: N 46 GLU cc_start: 0.7013 (mm-30) cc_final: 0.6635 (mm-30) outliers start: 33 outliers final: 13 residues processed: 163 average time/residue: 0.3435 time to fit residues: 60.0955 Evaluate side-chains 144 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 296 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 95 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN A 236 GLN A 239 ASN A 357 HIS G 18 GLN ** R 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.186022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.143616 restraints weight = 8956.298| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 2.70 r_work: 0.3814 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 8289 Z= 0.216 Angle : 0.679 11.736 11221 Z= 0.360 Chirality : 0.045 0.173 1280 Planarity : 0.005 0.040 1423 Dihedral : 4.647 22.196 1121 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.93 % Allowed : 22.25 % Favored : 73.82 % 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: 1.29 (0.26), residues: 1006 helix: 2.10 (0.25), residues: 406 sheet: 0.58 (0.35), residues: 194 loop : -0.24 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 38 TYR 0.021 0.002 TYR A 358 PHE 0.020 0.002 PHE B 199 TRP 0.019 0.003 TRP B 169 HIS 0.013 0.002 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.22 ( 8284) covalent geometry : angle 0.67922 / 0.36 (11210) SS BOND : bond 0.00348 / 0.17 ( 4) SS BOND : angle 0.76606 / 0.39 ( 8) hydrogen bonds : bond 0.05378 / 3.60 ( 441) hydrogen bonds : angle 4.62358 / 3.30 ( 1251) link_TRANS : bond 0.00150 / 0.08 ( 1) link_TRANS : angle 0.46456 / 0.43 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.6618 (tppp) REVERT: A 35 GLN cc_start: 0.7259 (OUTLIER) cc_final: 0.6650 (tm-30) REVERT: A 293 LYS cc_start: 0.8275 (mttt) cc_final: 0.6848 (tmtt) REVERT: A 339 TYR cc_start: 0.7859 (m-80) cc_final: 0.7614 (m-80) REVERT: A 342 ARG cc_start: 0.6977 (ttp-170) cc_final: 0.6318 (ttm-80) REVERT: B 16 ASN cc_start: 0.7797 (m-40) cc_final: 0.6852 (t0) REVERT: B 127 LYS cc_start: 0.6531 (mttp) cc_final: 0.6319 (mtmm) REVERT: B 175 GLN cc_start: 0.7506 (tp40) cc_final: 0.7137 (mm-40) REVERT: B 217 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.7339 (ptm) REVERT: B 239 ASN cc_start: 0.7368 (m110) cc_final: 0.6537 (t0) REVERT: B 251 ARG cc_start: 0.7996 (mtt180) cc_final: 0.7697 (mtt90) REVERT: B 336 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8086 (mt) REVERT: G 44 HIS cc_start: 0.6693 (m170) cc_final: 0.5917 (t-170) REVERT: N 46 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6779 (mm-30) outliers start: 35 outliers final: 17 residues processed: 150 average time/residue: 0.3790 time to fit residues: 60.9337 Evaluate side-chains 145 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 296 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 2.9990 chunk 47 optimal weight: 0.0970 chunk 16 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 236 GLN A 357 HIS R 264 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.189970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.147092 restraints weight = 8830.108| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 2.73 r_work: 0.3852 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.5441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8289 Z= 0.157 Angle : 0.631 12.109 11221 Z= 0.331 Chirality : 0.043 0.169 1280 Planarity : 0.004 0.044 1423 Dihedral : 4.468 19.271 1121 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.37 % Allowed : 23.03 % Favored : 73.60 % 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: 1006 helix: 2.23 (0.25), residues: 406 sheet: 0.61 (0.35), residues: 194 loop : -0.25 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 38 TYR 0.016 0.002 TYR N 95 PHE 0.016 0.002 PHE N 29 TRP 0.018 0.002 TRP B 169 HIS 0.013 0.002 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 8284) covalent geometry : angle 0.63070 / 0.33 (11210) SS BOND : bond 0.00286 / 0.14 ( 4) SS BOND : angle 0.57136 / 0.29 ( 8) hydrogen bonds : bond 0.04772 / 3.20 ( 441) hydrogen bonds : angle 4.45851 / 3.17 ( 1251) link_TRANS : bond 0.00036 / 0.02 ( 1) link_TRANS : angle 0.49227 / 0.44 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.6895 (tppt) REVERT: A 35 GLN cc_start: 0.7111 (OUTLIER) cc_final: 0.6813 (tp-100) REVERT: A 267 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7381 (tm-30) REVERT: A 293 LYS cc_start: 0.8309 (mttt) cc_final: 0.6928 (tmtt) REVERT: A 339 TYR cc_start: 0.7743 (m-80) cc_final: 0.7510 (m-80) REVERT: A 342 ARG cc_start: 0.6949 (ttp-170) cc_final: 0.6257 (ttm-80) REVERT: B 16 ASN cc_start: 0.7957 (m-40) cc_final: 0.6992 (t0) REVERT: B 175 GLN cc_start: 0.7504 (tp40) cc_final: 0.7103 (mm-40) REVERT: B 186 ASP cc_start: 0.5684 (OUTLIER) cc_final: 0.5453 (m-30) REVERT: B 217 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.7356 (ptm) REVERT: B 251 ARG cc_start: 0.7963 (mtt180) cc_final: 0.7654 (mtt90) REVERT: B 325 MET cc_start: 0.8601 (tpp) cc_final: 0.8381 (tpp) REVERT: B 336 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8043 (mt) REVERT: G 44 HIS cc_start: 0.6626 (m170) cc_final: 0.5958 (t-170) REVERT: N 38 ARG cc_start: 0.7105 (ttp80) cc_final: 0.6074 (tpp80) REVERT: N 46 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6549 (mm-30) REVERT: R 297 ILE cc_start: 0.7534 (OUTLIER) cc_final: 0.7003 (tp) outliers start: 30 outliers final: 15 residues processed: 148 average time/residue: 0.3812 time to fit residues: 60.6735 Evaluate side-chains 144 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 296 ILE Chi-restraints excluded: chain R residue 297 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 80 optimal weight: 0.8980 chunk 83 optimal weight: 0.1980 chunk 37 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 0.0000 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 236 GLN A 357 HIS R 264 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.194109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.151941 restraints weight = 8780.232| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 2.70 r_work: 0.3921 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.5543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8289 Z= 0.125 Angle : 0.623 14.350 11221 Z= 0.320 Chirality : 0.042 0.150 1280 Planarity : 0.004 0.045 1423 Dihedral : 4.215 19.582 1121 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.81 % Allowed : 24.61 % Favored : 72.58 % 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: 1.56 (0.26), residues: 1006 helix: 2.43 (0.25), residues: 403 sheet: 0.79 (0.36), residues: 192 loop : -0.24 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 38 TYR 0.014 0.001 TYR B 111 PHE 0.013 0.001 PHE B 253 TRP 0.019 0.002 TRP B 339 HIS 0.012 0.001 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 8284) covalent geometry : angle 0.62315 / 0.32 (11210) SS BOND : bond 0.00228 / 0.11 ( 4) SS BOND : angle 0.43336 / 0.24 ( 8) hydrogen bonds : bond 0.04191 / 2.82 ( 441) hydrogen bonds : angle 4.29247 / 3.04 ( 1251) link_TRANS : bond 0.00029 / 0.02 ( 1) link_TRANS : angle 0.41535 / 0.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7148 (OUTLIER) cc_final: 0.6844 (tppt) REVERT: A 267 GLN cc_start: 0.7964 (mm-40) cc_final: 0.7236 (tm-30) REVERT: A 293 LYS cc_start: 0.8318 (mttt) cc_final: 0.6892 (tmtt) REVERT: A 299 GLU cc_start: 0.8153 (pp20) cc_final: 0.7782 (pm20) REVERT: A 343 ASP cc_start: 0.8050 (m-30) cc_final: 0.7531 (p0) REVERT: B 16 ASN cc_start: 0.7973 (m-40) cc_final: 0.7029 (t0) REVERT: B 175 GLN cc_start: 0.7492 (tp40) cc_final: 0.7102 (mm-40) REVERT: B 251 ARG cc_start: 0.7938 (mtt180) cc_final: 0.7463 (mtm-85) REVERT: B 325 MET cc_start: 0.8656 (tpp) cc_final: 0.8449 (tpp) REVERT: G 44 HIS cc_start: 0.6556 (m170) cc_final: 0.6105 (t-170) REVERT: N 46 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6553 (mm-30) REVERT: R 273 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.6854 (mp10) outliers start: 25 outliers final: 14 residues processed: 150 average time/residue: 0.3887 time to fit residues: 62.5143 Evaluate side-chains 137 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 273 GLN Chi-restraints excluded: chain R residue 296 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 40 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 4 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN A 236 GLN A 357 HIS R 264 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.193406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.151575 restraints weight = 8797.711| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 2.66 r_work: 0.3909 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.5614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8289 Z= 0.130 Angle : 0.618 10.782 11221 Z= 0.323 Chirality : 0.042 0.170 1280 Planarity : 0.004 0.044 1423 Dihedral : 4.159 18.359 1121 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.25 % Allowed : 25.17 % Favored : 72.58 % 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: 1.66 (0.26), residues: 1006 helix: 2.49 (0.25), residues: 400 sheet: 0.80 (0.36), residues: 192 loop : -0.10 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 38 TYR 0.013 0.001 TYR B 111 PHE 0.020 0.001 PHE B 241 TRP 0.025 0.002 TRP B 339 HIS 0.013 0.001 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 8284) covalent geometry : angle 0.61791 / 0.32 (11210) SS BOND : bond 0.00233 / 0.12 ( 4) SS BOND : angle 0.46317 / 0.26 ( 8) hydrogen bonds : bond 0.04218 / 2.84 ( 441) hydrogen bonds : angle 4.30736 / 3.06 ( 1251) link_TRANS : bond 0.00017 / 0.01 ( 1) link_TRANS : angle 0.39814 / 0.37 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7155 (OUTLIER) cc_final: 0.6845 (tppt) REVERT: A 267 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7227 (tm-30) REVERT: A 293 LYS cc_start: 0.8247 (mttt) cc_final: 0.6873 (tmtt) REVERT: A 299 GLU cc_start: 0.8219 (pp20) cc_final: 0.7846 (pm20) REVERT: A 342 ARG cc_start: 0.6803 (ttp-170) cc_final: 0.6197 (ttm-80) REVERT: A 343 ASP cc_start: 0.8080 (m-30) cc_final: 0.7863 (m-30) REVERT: B 16 ASN cc_start: 0.7992 (m-40) cc_final: 0.7079 (t0) REVERT: B 175 GLN cc_start: 0.7550 (tp40) cc_final: 0.7180 (mm-40) REVERT: B 188 MET cc_start: 0.6870 (mmp) cc_final: 0.6543 (mmt) REVERT: B 217 MET cc_start: 0.7613 (ptm) cc_final: 0.7280 (ppp) REVERT: B 251 ARG cc_start: 0.7941 (mtt180) cc_final: 0.7505 (mtm-85) REVERT: G 44 HIS cc_start: 0.6482 (m170) cc_final: 0.6051 (t-170) REVERT: N 46 GLU cc_start: 0.6959 (mm-30) cc_final: 0.6504 (mm-30) REVERT: R 273 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6873 (mp10) REVERT: L 11 LYS cc_start: 0.8824 (mttp) cc_final: 0.8457 (mmtm) outliers start: 20 outliers final: 14 residues processed: 143 average time/residue: 0.4077 time to fit residues: 62.4427 Evaluate side-chains 141 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 273 GLN Chi-restraints excluded: chain R residue 296 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 33 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 43 optimal weight: 0.2980 chunk 53 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 13 optimal weight: 8.9990 chunk 70 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN A 236 GLN A 357 HIS R 264 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.195276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.154118 restraints weight = 8735.871| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 2.57 r_work: 0.3939 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.5722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8289 Z= 0.124 Angle : 0.627 13.211 11221 Z= 0.323 Chirality : 0.042 0.174 1280 Planarity : 0.004 0.045 1423 Dihedral : 4.101 19.015 1121 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.70 % Allowed : 25.06 % Favored : 72.25 % 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: 1.69 (0.27), residues: 1006 helix: 2.48 (0.25), residues: 403 sheet: 0.69 (0.36), residues: 204 loop : -0.01 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 38 TYR 0.014 0.001 TYR B 111 PHE 0.019 0.001 PHE B 241 TRP 0.025 0.002 TRP B 339 HIS 0.013 0.001 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 8284) covalent geometry : angle 0.62767 / 0.32 (11210) SS BOND : bond 0.00211 / 0.10 ( 4) SS BOND : angle 0.42096 / 0.23 ( 8) hydrogen bonds : bond 0.04086 / 2.76 ( 441) hydrogen bonds : angle 4.27988 / 3.05 ( 1251) link_TRANS : bond 0.00037 / 0.02 ( 1) link_TRANS : angle 0.37916 / 0.35 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2367.07 seconds wall clock time: 41 minutes 2.04 seconds (2462.04 seconds total)