Starting phenix.real_space_refine on Tue Mar 3 18:56:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f54_31457/03_2026/7f54_31457.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f54_31457/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7f54_31457/03_2026/7f54_31457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f54_31457/03_2026/7f54_31457.map" model { file = "/net/cci-nas-00/data/ceres_data/7f54_31457/03_2026/7f54_31457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f54_31457/03_2026/7f54_31457.cif" } 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-5986/lib/python3.9/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} Modifications used: {'PEPT-D': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5} 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: 1.99, per 1000 atoms: 0.24 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: 1.03 Conformation dependent library (CDL) restraints added in 330.3 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: 0.25 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: 1.51 Time building geometry restraints manager: 1.26 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: 4657 17.58 - 35.16: 227 35.16 - 52.74: 49 52.74 - 70.32: 19 70.32 - 87.91: 5 Dihedral angle restraints: 4957 sinusoidal: 1950 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 4954 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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.920 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6362 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= 0.555 Chirality : 0.053 0.277 1280 Planarity : 0.006 0.041 1423 Dihedral : 11.933 87.906 2994 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 covalent geometry : bond 0.00443 ( 8284) covalent geometry : angle 0.89157 (11210) SS BOND : bond 0.00655 ( 4) SS BOND : angle 3.16046 ( 8) hydrogen bonds : bond 0.14710 ( 441) hydrogen bonds : angle 6.27302 ( 1251) link_TRANS : bond 0.00506 ( 1) link_TRANS : angle 0.63596 ( 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 : 0.240 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: 0.5816 (p0) REVERT: B 265 SER cc_start: 0.7898 (p) cc_final: 0.7548 (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: 0.4831 time to fit residues: 122.9665 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 : 0.331 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.199435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.156855 restraints weight = 8705.700| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 2.66 r_work: 0.4009 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8289 Z= 0.147 Angle : 0.592 7.736 11221 Z= 0.323 Chirality : 0.042 0.165 1280 Planarity : 0.004 0.036 1423 Dihedral : 4.225 15.784 1125 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.48 % Allowed : 13.37 % Favored : 83.15 % 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: 1.99 (0.26), residues: 1006 helix: 2.22 (0.24), residues: 412 sheet: 1.18 (0.33), residues: 220 loop : 0.49 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 197 TYR 0.015 0.001 TYR B 85 PHE 0.017 0.002 PHE N 68 TRP 0.017 0.002 TRP B 169 HIS 0.009 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8284) covalent geometry : angle 0.59204 (11210) SS BOND : bond 0.00343 ( 4) SS BOND : angle 0.64226 ( 8) hydrogen bonds : bond 0.05156 ( 441) hydrogen bonds : angle 4.54996 ( 1251) link_TRANS : bond 0.00043 ( 1) link_TRANS : angle 0.28089 ( 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 191 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7109 (OUTLIER) cc_final: 0.6798 (tp-100) REVERT: A 289 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7523 (tt) REVERT: A 293 LYS cc_start: 0.8477 (mttt) cc_final: 0.7196 (tmtt) REVERT: A 343 ASP cc_start: 0.7889 (m-30) cc_final: 0.7404 (p0) REVERT: A 346 LEU cc_start: 0.7410 (mt) cc_final: 0.7145 (mt) REVERT: A 364 THR cc_start: 0.6730 (p) cc_final: 0.6405 (t) REVERT: A 374 ARG cc_start: 0.8203 (mtt180) cc_final: 0.7961 (mtm-85) REVERT: B 20 ASP cc_start: 0.6728 (m-30) cc_final: 0.6123 (p0) REVERT: B 186 ASP cc_start: 0.5705 (OUTLIER) cc_final: 0.5392 (m-30) REVERT: B 217 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.7104 (ptm) REVERT: B 280 LYS cc_start: 0.8211 (tttt) cc_final: 0.7875 (tttt) REVERT: B 325 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.8028 (tpp) REVERT: G 16 VAL cc_start: 0.6985 (m) cc_final: 0.6625 (t) REVERT: G 19 LEU cc_start: 0.5924 (mp) cc_final: 0.5563 (mp) REVERT: G 44 HIS cc_start: 0.5868 (m170) cc_final: 0.5116 (t-170) REVERT: N 43 LYS cc_start: 0.6717 (mmtt) cc_final: 0.6516 (mmtt) REVERT: N 77 ASN cc_start: 0.7789 (m-40) cc_final: 0.7420 (t0) outliers start: 31 outliers final: 11 residues processed: 181 average time/residue: 0.4588 time to fit residues: 89.0466 Evaluate side-chains 147 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 289 LEU 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 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 296 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: 0.9990 chunk 58 optimal weight: 5.9990 chunk 14 optimal weight: 0.1980 chunk 87 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 76 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 259 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 = 0.4552 r_free = 0.4552 target = 0.200542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.158384 restraints weight = 8727.783| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 2.67 r_work: 0.3984 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8289 Z= 0.120 Angle : 0.538 7.663 11221 Z= 0.290 Chirality : 0.041 0.138 1280 Planarity : 0.004 0.034 1423 Dihedral : 4.118 17.752 1124 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 4.16 % Allowed : 15.39 % Favored : 80.45 % 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: 2.04 (0.26), residues: 1006 helix: 2.43 (0.24), residues: 412 sheet: 1.19 (0.32), residues: 222 loop : 0.30 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 380 TYR 0.012 0.001 TYR R 268 PHE 0.027 0.002 PHE B 241 TRP 0.016 0.002 TRP B 211 HIS 0.007 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 8284) covalent geometry : angle 0.53828 (11210) SS BOND : bond 0.00264 ( 4) SS BOND : angle 0.50109 ( 8) hydrogen bonds : bond 0.04498 ( 441) hydrogen bonds : angle 4.27903 ( 1251) link_TRANS : bond 0.00006 ( 1) link_TRANS : angle 0.34830 ( 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 185 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7084 (OUTLIER) cc_final: 0.6705 (tppt) REVERT: A 293 LYS cc_start: 0.8455 (mttt) cc_final: 0.7092 (tmtt) REVERT: A 346 LEU cc_start: 0.7510 (mt) cc_final: 0.7221 (mt) REVERT: A 364 THR cc_start: 0.7035 (p) cc_final: 0.6775 (t) REVERT: A 374 ARG cc_start: 0.8255 (mtt180) cc_final: 0.7966 (mtm-85) REVERT: B 20 ASP cc_start: 0.6743 (m-30) cc_final: 0.6193 (p0) REVERT: B 175 GLN cc_start: 0.6691 (tp40) cc_final: 0.6335 (mm-40) REVERT: B 217 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.7147 (ptm) REVERT: B 251 ARG cc_start: 0.7513 (mtm-85) cc_final: 0.7204 (mtm-85) REVERT: B 325 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.8062 (tpp) REVERT: G 16 VAL cc_start: 0.7029 (m) cc_final: 0.6722 (t) REVERT: G 44 HIS cc_start: 0.6008 (m170) cc_final: 0.5496 (t-170) REVERT: N 98 ARG cc_start: 0.7488 (ttp80) cc_final: 0.7235 (ttp-170) REVERT: R 204 MET cc_start: 0.6429 (mtm) cc_final: 0.5543 (mmt) outliers start: 37 outliers final: 13 residues processed: 168 average time/residue: 0.4248 time to fit residues: 76.9251 Evaluate side-chains 148 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 214 VAL 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 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 325 MET Chi-restraints excluded: chain R residue 93 VAL 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: 0.9990 chunk 31 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 25 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 5 optimal weight: 0.0980 chunk 21 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 220 HIS A 292 ASN A 390 GLN R 76 HIS R 264 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.196280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.154559 restraints weight = 8924.887| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 2.54 r_work: 0.3969 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8289 Z= 0.120 Angle : 0.540 8.774 11221 Z= 0.286 Chirality : 0.042 0.145 1280 Planarity : 0.004 0.033 1423 Dihedral : 4.078 19.191 1122 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 4.04 % Allowed : 16.18 % Favored : 79.78 % 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: 2.03 (0.26), residues: 1006 helix: 2.46 (0.25), residues: 406 sheet: 1.31 (0.34), residues: 208 loop : 0.23 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 380 TYR 0.011 0.001 TYR B 111 PHE 0.019 0.001 PHE A 376 TRP 0.016 0.002 TRP B 339 HIS 0.006 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8284) covalent geometry : angle 0.54035 (11210) SS BOND : bond 0.00258 ( 4) SS BOND : angle 0.46313 ( 8) hydrogen bonds : bond 0.04337 ( 441) hydrogen bonds : angle 4.18803 ( 1251) link_TRANS : bond 0.00023 ( 1) link_TRANS : angle 0.38622 ( 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 176 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7198 (OUTLIER) cc_final: 0.6840 (tppt) REVERT: A 293 LYS cc_start: 0.8341 (mttt) cc_final: 0.6982 (tmtt) REVERT: A 342 ARG cc_start: 0.6811 (ttp-170) cc_final: 0.6072 (ttm-80) REVERT: A 346 LEU cc_start: 0.7670 (mt) cc_final: 0.7403 (mt) REVERT: A 364 THR cc_start: 0.6933 (p) cc_final: 0.6653 (t) REVERT: A 374 ARG cc_start: 0.8073 (mtt180) cc_final: 0.7832 (mtm-85) REVERT: B 175 GLN cc_start: 0.6813 (tp40) cc_final: 0.6561 (mm-40) REVERT: B 186 ASP cc_start: 0.5618 (OUTLIER) cc_final: 0.5396 (m-30) REVERT: B 217 MET cc_start: 0.7443 (OUTLIER) cc_final: 0.7206 (ptm) REVERT: B 275 SER cc_start: 0.6954 (m) cc_final: 0.6553 (p) REVERT: B 325 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8136 (tpp) REVERT: B 336 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8071 (mt) REVERT: G 44 HIS cc_start: 0.6074 (m170) cc_final: 0.5605 (t-170) REVERT: N 38 ARG cc_start: 0.6927 (ttm170) cc_final: 0.6724 (ttp80) REVERT: N 46 GLU cc_start: 0.6785 (mt-10) cc_final: 0.6570 (mm-30) REVERT: R 297 ILE cc_start: 0.7296 (OUTLIER) cc_final: 0.6728 (tp) outliers start: 36 outliers final: 15 residues processed: 161 average time/residue: 0.4879 time to fit residues: 83.9596 Evaluate side-chains 155 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 263 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 348 ILE 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 325 MET 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 103 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: 0.1980 chunk 70 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 25 optimal weight: 0.0870 chunk 96 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 41 HIS A 292 ASN R 264 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.199743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.157155 restraints weight = 8853.072| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 2.69 r_work: 0.3964 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8289 Z= 0.111 Angle : 0.530 8.240 11221 Z= 0.281 Chirality : 0.041 0.151 1280 Planarity : 0.004 0.036 1423 Dihedral : 3.973 14.280 1122 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.37 % Allowed : 17.98 % Favored : 78.65 % 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: 2.07 (0.26), residues: 1006 helix: 2.54 (0.25), residues: 407 sheet: 1.31 (0.35), residues: 202 loop : 0.23 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 98 TYR 0.012 0.001 TYR R 268 PHE 0.011 0.001 PHE B 199 TRP 0.019 0.002 TRP B 339 HIS 0.005 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 8284) covalent geometry : angle 0.52996 (11210) SS BOND : bond 0.00232 ( 4) SS BOND : angle 0.51317 ( 8) hydrogen bonds : bond 0.04080 ( 441) hydrogen bonds : angle 4.08681 ( 1251) link_TRANS : bond 0.00057 ( 1) link_TRANS : angle 0.37131 ( 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 172 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7082 (OUTLIER) cc_final: 0.6719 (tppt) REVERT: A 293 LYS cc_start: 0.8303 (mttt) cc_final: 0.6957 (tmtt) REVERT: A 342 ARG cc_start: 0.6780 (ttp-170) cc_final: 0.5958 (ttm-80) REVERT: A 346 LEU cc_start: 0.7603 (mt) cc_final: 0.7326 (mt) REVERT: A 364 THR cc_start: 0.7018 (p) cc_final: 0.6753 (t) REVERT: B 16 ASN cc_start: 0.7542 (m-40) cc_final: 0.6628 (t160) REVERT: B 175 GLN cc_start: 0.7043 (tp40) cc_final: 0.6765 (mm-40) REVERT: B 186 ASP cc_start: 0.5527 (OUTLIER) cc_final: 0.5284 (m-30) REVERT: B 217 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.7178 (ptm) REVERT: B 275 SER cc_start: 0.6832 (m) cc_final: 0.6414 (p) REVERT: B 336 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8069 (mt) REVERT: G 44 HIS cc_start: 0.6086 (m170) cc_final: 0.5535 (t-90) REVERT: N 46 GLU cc_start: 0.6770 (mt-10) cc_final: 0.6423 (mm-30) REVERT: R 79 MET cc_start: 0.5389 (ptm) cc_final: 0.4088 (tmm) REVERT: R 281 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7717 (mpt) REVERT: R 292 MET cc_start: 0.6666 (OUTLIER) cc_final: 0.6318 (mtt) outliers start: 30 outliers final: 14 residues processed: 159 average time/residue: 0.4530 time to fit residues: 77.2927 Evaluate side-chains 150 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 263 THR Chi-restraints excluded: chain A residue 348 ILE 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 336 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 281 MET Chi-restraints excluded: chain R residue 292 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 30 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 97 optimal weight: 0.0870 chunk 2 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 35 optimal weight: 0.3980 chunk 16 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.199531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.157586 restraints weight = 8700.175| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 2.64 r_work: 0.3981 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8289 Z= 0.117 Angle : 0.561 13.561 11221 Z= 0.292 Chirality : 0.041 0.155 1280 Planarity : 0.003 0.034 1423 Dihedral : 3.935 14.315 1122 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.81 % Allowed : 19.55 % Favored : 77.64 % 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: 2.48 (0.25), residues: 407 sheet: 1.29 (0.35), residues: 202 loop : 0.19 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 232 TYR 0.015 0.001 TYR B 111 PHE 0.012 0.001 PHE B 199 TRP 0.022 0.002 TRP B 339 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8284) covalent geometry : angle 0.56080 (11210) SS BOND : bond 0.00206 ( 4) SS BOND : angle 0.46016 ( 8) hydrogen bonds : bond 0.04081 ( 441) hydrogen bonds : angle 4.13250 ( 1251) link_TRANS : bond 0.00075 ( 1) link_TRANS : angle 0.40124 ( 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 163 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7111 (OUTLIER) cc_final: 0.6562 (tppp) REVERT: A 293 LYS cc_start: 0.8336 (mttt) cc_final: 0.7019 (tmtt) REVERT: A 299 GLU cc_start: 0.8143 (pp20) cc_final: 0.7870 (pm20) REVERT: A 342 ARG cc_start: 0.6736 (ttp-170) cc_final: 0.5842 (ttm-80) REVERT: A 346 LEU cc_start: 0.7659 (mt) cc_final: 0.7342 (mt) REVERT: A 364 THR cc_start: 0.7106 (p) cc_final: 0.6869 (t) REVERT: B 98 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8225 (t) REVERT: B 175 GLN cc_start: 0.6995 (tp40) cc_final: 0.6727 (mm-40) REVERT: B 186 ASP cc_start: 0.5429 (OUTLIER) cc_final: 0.5206 (m-30) REVERT: B 275 SER cc_start: 0.6985 (m) cc_final: 0.6519 (p) REVERT: B 336 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8049 (mt) REVERT: G 44 HIS cc_start: 0.6030 (m170) cc_final: 0.5539 (t-90) REVERT: N 46 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6524 (mm-30) REVERT: R 79 MET cc_start: 0.5416 (ptm) cc_final: 0.4027 (tmm) REVERT: R 281 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7672 (mpt) REVERT: R 297 ILE cc_start: 0.7277 (OUTLIER) cc_final: 0.6743 (tp) outliers start: 25 outliers final: 11 residues processed: 152 average time/residue: 0.4772 time to fit residues: 77.7832 Evaluate side-chains 146 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 263 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 186 ASP 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 B residue 336 LEU Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 281 MET Chi-restraints excluded: chain R residue 297 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 95 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 37 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 292 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.198129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.156217 restraints weight = 8855.991| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 2.61 r_work: 0.3963 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8289 Z= 0.120 Angle : 0.569 8.751 11221 Z= 0.299 Chirality : 0.042 0.157 1280 Planarity : 0.004 0.033 1423 Dihedral : 3.990 14.997 1122 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.26 % Allowed : 19.66 % Favored : 77.08 % 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: 1.99 (0.26), residues: 1006 helix: 2.49 (0.25), residues: 407 sheet: 1.32 (0.36), residues: 198 loop : 0.12 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 38 TYR 0.015 0.001 TYR B 111 PHE 0.012 0.001 PHE B 199 TRP 0.028 0.002 TRP B 339 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8284) covalent geometry : angle 0.56866 (11210) SS BOND : bond 0.00201 ( 4) SS BOND : angle 0.49296 ( 8) hydrogen bonds : bond 0.04111 ( 441) hydrogen bonds : angle 4.15005 ( 1251) link_TRANS : bond 0.00048 ( 1) link_TRANS : angle 0.42446 ( 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 166 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7099 (OUTLIER) cc_final: 0.6552 (tppp) REVERT: A 293 LYS cc_start: 0.8371 (mttt) cc_final: 0.6989 (tmtt) REVERT: A 299 GLU cc_start: 0.8172 (pp20) cc_final: 0.7961 (pm20) REVERT: A 342 ARG cc_start: 0.6739 (ttp-170) cc_final: 0.5888 (ttm-80) REVERT: A 346 LEU cc_start: 0.7662 (mt) cc_final: 0.7345 (mt) REVERT: A 364 THR cc_start: 0.7031 (p) cc_final: 0.6763 (t) REVERT: B 16 ASN cc_start: 0.7641 (m-40) cc_final: 0.6650 (t160) REVERT: B 44 GLN cc_start: 0.8144 (tp40) cc_final: 0.7868 (tp40) REVERT: B 98 SER cc_start: 0.8823 (OUTLIER) cc_final: 0.8250 (t) REVERT: B 175 GLN cc_start: 0.7135 (tp40) cc_final: 0.6818 (mm-40) REVERT: B 186 ASP cc_start: 0.5447 (OUTLIER) cc_final: 0.5167 (m-30) REVERT: B 188 MET cc_start: 0.6879 (mmp) cc_final: 0.6596 (mmt) REVERT: B 217 MET cc_start: 0.7560 (ptm) cc_final: 0.7034 (pmt) REVERT: B 251 ARG cc_start: 0.7584 (mtm-85) cc_final: 0.7035 (ttm110) REVERT: B 275 SER cc_start: 0.7043 (m) cc_final: 0.6625 (p) REVERT: B 291 ASP cc_start: 0.6613 (m-30) cc_final: 0.6090 (m-30) REVERT: B 336 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8047 (mt) REVERT: G 44 HIS cc_start: 0.6134 (m170) cc_final: 0.5651 (t-90) REVERT: N 46 GLU cc_start: 0.6915 (mt-10) cc_final: 0.6460 (mm-30) REVERT: R 79 MET cc_start: 0.5537 (ptm) cc_final: 0.5207 (ptp) REVERT: R 273 GLN cc_start: 0.6976 (OUTLIER) cc_final: 0.6674 (mp10) REVERT: R 281 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7750 (mpt) REVERT: R 297 ILE cc_start: 0.7310 (OUTLIER) cc_final: 0.6848 (tp) outliers start: 29 outliers final: 12 residues processed: 154 average time/residue: 0.4696 time to fit residues: 77.7230 Evaluate side-chains 146 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 263 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 348 ILE 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 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 273 GLN Chi-restraints excluded: chain R residue 281 MET Chi-restraints excluded: chain R residue 297 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 90 optimal weight: 0.0470 chunk 52 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.197167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.155319 restraints weight = 8800.205| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 2.59 r_work: 0.3942 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8289 Z= 0.131 Angle : 0.586 11.731 11221 Z= 0.307 Chirality : 0.042 0.165 1280 Planarity : 0.004 0.034 1423 Dihedral : 4.071 17.006 1122 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.81 % Allowed : 20.90 % Favored : 76.29 % 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: 1.92 (0.26), residues: 1006 helix: 2.46 (0.25), residues: 407 sheet: 1.25 (0.35), residues: 204 loop : 0.06 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 38 TYR 0.013 0.001 TYR N 95 PHE 0.013 0.001 PHE N 29 TRP 0.028 0.002 TRP B 339 HIS 0.004 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8284) covalent geometry : angle 0.58638 (11210) SS BOND : bond 0.00217 ( 4) SS BOND : angle 0.49939 ( 8) hydrogen bonds : bond 0.04286 ( 441) hydrogen bonds : angle 4.19963 ( 1251) link_TRANS : bond 0.00033 ( 1) link_TRANS : angle 0.46408 ( 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 164 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7151 (OUTLIER) cc_final: 0.6560 (tppp) REVERT: A 293 LYS cc_start: 0.8268 (mttt) cc_final: 0.6939 (tmtt) REVERT: A 342 ARG cc_start: 0.6710 (ttp-170) cc_final: 0.6035 (ttm-80) REVERT: A 364 THR cc_start: 0.7211 (p) cc_final: 0.6890 (t) REVERT: B 16 ASN cc_start: 0.7657 (m-40) cc_final: 0.6665 (t160) REVERT: B 98 SER cc_start: 0.8903 (OUTLIER) cc_final: 0.8334 (t) REVERT: B 175 GLN cc_start: 0.7161 (tp40) cc_final: 0.6851 (mm-40) REVERT: B 186 ASP cc_start: 0.5386 (OUTLIER) cc_final: 0.5171 (m-30) REVERT: B 275 SER cc_start: 0.7101 (m) cc_final: 0.6725 (p) REVERT: B 336 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8055 (mt) REVERT: G 44 HIS cc_start: 0.6193 (m170) cc_final: 0.5693 (t-90) REVERT: N 46 GLU cc_start: 0.6895 (mt-10) cc_final: 0.6503 (mm-30) REVERT: R 273 GLN cc_start: 0.7089 (OUTLIER) cc_final: 0.6754 (mp10) REVERT: R 281 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7822 (mpt) outliers start: 25 outliers final: 13 residues processed: 157 average time/residue: 0.4516 time to fit residues: 76.1445 Evaluate side-chains 147 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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 263 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 348 ILE 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 186 ASP 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 336 LEU Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 273 GLN Chi-restraints excluded: chain R residue 281 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 80 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 91 optimal weight: 0.1980 chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 292 ASN B 176 GLN R 264 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.198143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.156343 restraints weight = 8792.162| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 2.59 r_work: 0.3967 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8289 Z= 0.124 Angle : 0.622 14.499 11221 Z= 0.319 Chirality : 0.042 0.165 1280 Planarity : 0.004 0.034 1423 Dihedral : 4.040 17.974 1122 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.70 % Allowed : 21.91 % Favored : 75.39 % 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: 1.95 (0.26), residues: 1006 helix: 2.49 (0.25), residues: 403 sheet: 1.32 (0.37), residues: 194 loop : 0.10 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 38 TYR 0.015 0.001 TYR B 111 PHE 0.020 0.001 PHE B 253 TRP 0.034 0.002 TRP B 339 HIS 0.007 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 8284) covalent geometry : angle 0.62238 (11210) SS BOND : bond 0.00218 ( 4) SS BOND : angle 0.45981 ( 8) hydrogen bonds : bond 0.04205 ( 441) hydrogen bonds : angle 4.22454 ( 1251) link_TRANS : bond 0.00024 ( 1) link_TRANS : angle 0.41848 ( 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 147 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7133 (OUTLIER) cc_final: 0.6828 (tppt) REVERT: A 293 LYS cc_start: 0.8161 (mttt) cc_final: 0.6792 (tmtt) REVERT: A 342 ARG cc_start: 0.6705 (ttp-170) cc_final: 0.6067 (ttm-80) REVERT: A 364 THR cc_start: 0.7212 (p) cc_final: 0.6887 (t) REVERT: B 16 ASN cc_start: 0.7639 (m-40) cc_final: 0.6647 (t160) REVERT: B 45 MET cc_start: 0.7742 (mpt) cc_final: 0.7483 (mtm) REVERT: B 98 SER cc_start: 0.8907 (OUTLIER) cc_final: 0.8374 (t) REVERT: B 175 GLN cc_start: 0.7208 (tp40) cc_final: 0.6910 (mm-40) REVERT: B 186 ASP cc_start: 0.5291 (OUTLIER) cc_final: 0.5063 (m-30) REVERT: B 275 SER cc_start: 0.6922 (m) cc_final: 0.6543 (p) REVERT: B 336 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8059 (mt) REVERT: G 44 HIS cc_start: 0.6148 (m170) cc_final: 0.5688 (t-90) REVERT: N 46 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6448 (mm-30) REVERT: R 79 MET cc_start: 0.5231 (ptm) cc_final: 0.3987 (tmm) REVERT: R 204 MET cc_start: 0.5722 (mtp) cc_final: 0.5182 (pp-130) REVERT: R 273 GLN cc_start: 0.7087 (OUTLIER) cc_final: 0.6771 (mp10) REVERT: R 281 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7790 (mpt) outliers start: 24 outliers final: 13 residues processed: 141 average time/residue: 0.4508 time to fit residues: 68.3985 Evaluate side-chains 139 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 263 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 348 ILE 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 186 ASP 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 336 LEU Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 273 GLN Chi-restraints excluded: chain R residue 281 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 73 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 70 optimal weight: 0.0470 chunk 84 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 292 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.197474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.156267 restraints weight = 8852.244| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 2.58 r_work: 0.3964 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.5212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8289 Z= 0.127 Angle : 0.641 14.273 11221 Z= 0.328 Chirality : 0.042 0.172 1280 Planarity : 0.003 0.034 1423 Dihedral : 4.023 19.278 1122 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.25 % Allowed : 22.81 % Favored : 74.94 % 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: 1.96 (0.26), residues: 1006 helix: 2.48 (0.25), residues: 403 sheet: 1.43 (0.37), residues: 192 loop : 0.07 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 38 TYR 0.011 0.001 TYR N 95 PHE 0.013 0.001 PHE N 29 TRP 0.034 0.002 TRP B 339 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8284) covalent geometry : angle 0.64153 (11210) SS BOND : bond 0.00206 ( 4) SS BOND : angle 0.45568 ( 8) hydrogen bonds : bond 0.04174 ( 441) hydrogen bonds : angle 4.33478 ( 1251) link_TRANS : bond 0.00027 ( 1) link_TRANS : angle 0.40713 ( 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 158 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7150 (OUTLIER) cc_final: 0.6840 (tppt) REVERT: A 293 LYS cc_start: 0.8249 (mttt) cc_final: 0.6902 (tmtt) REVERT: A 342 ARG cc_start: 0.6675 (ttp-170) cc_final: 0.6000 (ttm-80) REVERT: A 343 ASP cc_start: 0.8079 (m-30) cc_final: 0.7770 (m-30) REVERT: A 364 THR cc_start: 0.7290 (p) cc_final: 0.6939 (t) REVERT: B 16 ASN cc_start: 0.7673 (m-40) cc_final: 0.6733 (t160) REVERT: B 45 MET cc_start: 0.7823 (mpt) cc_final: 0.7558 (mtm) REVERT: B 88 ASN cc_start: 0.7923 (m110) cc_final: 0.7600 (p0) REVERT: B 175 GLN cc_start: 0.7304 (tp40) cc_final: 0.7038 (mm-40) REVERT: B 186 ASP cc_start: 0.5208 (OUTLIER) cc_final: 0.5002 (m-30) REVERT: B 275 SER cc_start: 0.6915 (m) cc_final: 0.6491 (p) REVERT: B 336 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8057 (mt) REVERT: G 44 HIS cc_start: 0.6211 (m170) cc_final: 0.5777 (t-90) REVERT: N 46 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6515 (mm-30) REVERT: R 79 MET cc_start: 0.5275 (ptm) cc_final: 0.4020 (tmm) REVERT: R 204 MET cc_start: 0.5628 (mtp) cc_final: 0.5229 (pp-130) REVERT: R 273 GLN cc_start: 0.7093 (OUTLIER) cc_final: 0.6767 (mp10) REVERT: R 281 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7823 (mpt) outliers start: 20 outliers final: 14 residues processed: 152 average time/residue: 0.4506 time to fit residues: 73.5840 Evaluate side-chains 149 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 263 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 348 ILE 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 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 273 GLN Chi-restraints excluded: chain R residue 281 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 33 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4506 r_free = 0.4506 target = 0.194737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.153931 restraints weight = 8811.499| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 2.52 r_work: 0.3951 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.5286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8289 Z= 0.137 Angle : 0.663 13.821 11221 Z= 0.339 Chirality : 0.042 0.170 1280 Planarity : 0.004 0.040 1423 Dihedral : 4.074 19.119 1122 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.36 % Allowed : 23.26 % Favored : 74.38 % 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: 1.92 (0.26), residues: 1006 helix: 2.47 (0.25), residues: 403 sheet: 1.31 (0.37), residues: 194 loop : 0.08 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 20 TYR 0.013 0.001 TYR B 111 PHE 0.018 0.001 PHE B 241 TRP 0.038 0.002 TRP B 339 HIS 0.012 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8284) covalent geometry : angle 0.66286 (11210) SS BOND : bond 0.00227 ( 4) SS BOND : angle 0.51408 ( 8) hydrogen bonds : bond 0.04380 ( 441) hydrogen bonds : angle 4.36259 ( 1251) link_TRANS : bond 0.00017 ( 1) link_TRANS : angle 0.42989 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3090.44 seconds wall clock time: 53 minutes 15.90 seconds (3195.90 seconds total)