Starting phenix.real_space_refine on Thu Jul 2 13:17:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xw9_33494/07_2026/7xw9_33494.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xw9_33494/07_2026/7xw9_33494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7xw9_33494/07_2026/7xw9_33494.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xw9_33494/07_2026/7xw9_33494.cif" model { file = "/net/cci-nas-00/data/ceres_data/7xw9_33494/07_2026/7xw9_33494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xw9_33494/07_2026/7xw9_33494.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xw9_33494/07_2026/7xw9_33494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xw9_33494/07_2026/7xw9_33494.map" } resolution = 2.7 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= 0.002 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5729 2.51 5 N 1533 2.21 5 O 1663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s 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: 8988 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2294 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1862 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "S" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "L" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Classifications: {'peptide': 3} Link IDs: {'PTRANS': 1, 'TRANS': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.19, per 1000 atoms: 0.24 Number of scatterers: 8988 At special positions: 0 Unit cell: (116.61, 111.54, 123.708, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1663 8.00 N 1533 7.00 C 5729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 179 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 346.1 milliseconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 37.9% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'R' and resid 23 through 53 Processing helix chain 'R' and resid 58 through 79 Processing helix chain 'R' and resid 79 through 89 removed outlier: 3.782A pdb=" N ILE R 83 " --> pdb=" O GLY R 79 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR R 84 " --> pdb=" O LEU R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 129 removed outlier: 4.031A pdb=" N SER R 113 " --> pdb=" O ILE R 109 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 137 Processing helix chain 'R' and resid 138 through 162 removed outlier: 3.837A pdb=" N TYR R 156 " --> pdb=" O PHE R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 184 through 187 Processing helix chain 'R' and resid 188 through 220 Proline residue: R 203 - end of helix removed outlier: 3.553A pdb=" N LEU R 220 " --> pdb=" O ARG R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 290 removed outlier: 4.051A pdb=" N GLN R 263 " --> pdb=" O SER R 259 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL R 264 " --> pdb=" O SER R 260 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR R 265 " --> pdb=" O ARG R 261 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS R 266 " --> pdb=" O LYS R 262 " (cutoff:3.500A) Proline residue: R 281 - end of helix removed outlier: 3.648A pdb=" N SER R 290 " --> pdb=" O VAL R 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 321 Proline residue: R 317 - end of helix Processing helix chain 'R' and resid 325 through 335 Processing helix chain 'A' and resid 6 through 32 removed outlier: 4.143A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 removed outlier: 4.236A pdb=" N GLY A 45 " --> pdb=" O GLY A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 264 removed outlier: 3.733A pdb=" N GLN A 261 " --> pdb=" O LYS A 258 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN A 264 " --> pdb=" O GLN A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 293 Processing helix chain 'A' and resid 308 through 319 removed outlier: 3.903A pdb=" N LEU A 312 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 327 removed outlier: 4.067A pdb=" N TYR A 326 " --> pdb=" O LYS A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 366 removed outlier: 3.542A pdb=" N THR A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 406 removed outlier: 3.560A pdb=" N ARG A 404 " --> pdb=" O GLN A 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.592A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.550A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.517A pdb=" N ASP S 211 " --> pdb=" O GLU S 208 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 208 through 212' Processing sheet with id=AA1, first strand: chain 'R' and resid 164 through 168 Processing sheet with id=AA2, first strand: chain 'A' and resid 232 through 239 removed outlier: 4.631A pdb=" N VAL A 249 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LYS A 35 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE A 270 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU A 37 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL A 272 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A 39 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N ASP A 274 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.508A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.665A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.843A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.552A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.729A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.414A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.890A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.513A pdb=" N THR S 78 " --> pdb=" O ASP S 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.978A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 removed outlier: 3.635A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.482A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 453 hydrogen bonds defined for protein. 1272 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: 1.42 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 1449 1.30 - 1.43: 2504 1.43 - 1.57: 5132 1.57 - 1.70: 0 1.70 - 1.83: 91 Bond restraints: 9176 Sorted by residual: bond pdb=" CG PCA L 1 " pdb=" CD PCA L 1 " ideal model delta sigma weight residual 1.517 1.420 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" CA HIS L 2 " pdb=" C HIS L 2 " ideal model delta sigma weight residual 1.525 1.424 0.101 2.10e-02 2.27e+03 2.29e+01 bond pdb=" N PCA L 1 " pdb=" CD PCA L 1 " ideal model delta sigma weight residual 1.345 1.253 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" N PCA L 1 " pdb=" CA PCA L 1 " ideal model delta sigma weight residual 1.458 1.379 0.079 1.90e-02 2.77e+03 1.73e+01 bond pdb=" CA PCA L 1 " pdb=" CB PCA L 1 " ideal model delta sigma weight residual 1.530 1.456 0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 9171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 12332 2.96 - 5.92: 88 5.92 - 8.88: 12 8.88 - 11.84: 1 11.84 - 14.80: 1 Bond angle restraints: 12434 Sorted by residual: angle pdb=" N SER A 44 " pdb=" CA SER A 44 " pdb=" C SER A 44 " ideal model delta sigma weight residual 111.28 126.08 -14.80 1.09e+00 8.42e-01 1.84e+02 angle pdb=" C VAL R 201 " pdb=" N VAL R 202 " pdb=" CA VAL R 202 " ideal model delta sigma weight residual 122.13 113.55 8.58 1.85e+00 2.92e-01 2.15e+01 angle pdb=" C GLU A 43 " pdb=" N SER A 44 " pdb=" CA SER A 44 " ideal model delta sigma weight residual 120.28 126.31 -6.03 1.34e+00 5.57e-01 2.02e+01 angle pdb=" N TRP R 300 " pdb=" CA TRP R 300 " pdb=" C TRP R 300 " ideal model delta sigma weight residual 114.56 109.00 5.56 1.27e+00 6.20e-01 1.92e+01 angle pdb=" N PCA L 1 " pdb=" CA PCA L 1 " pdb=" CB PCA L 1 " ideal model delta sigma weight residual 110.50 103.75 6.75 1.70e+00 3.46e-01 1.58e+01 ... (remaining 12429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 4916 15.42 - 30.85: 426 30.85 - 46.27: 85 46.27 - 61.70: 18 61.70 - 77.12: 6 Dihedral angle restraints: 5451 sinusoidal: 2129 harmonic: 3322 Sorted by residual: dihedral pdb=" CA LEU R 22 " pdb=" C LEU R 22 " pdb=" N GLU R 23 " pdb=" CA GLU R 23 " ideal model delta harmonic sigma weight residual 180.00 156.11 23.89 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA TYR S 101 " pdb=" C TYR S 101 " pdb=" N TYR S 102 " pdb=" CA TYR S 102 " ideal model delta harmonic sigma weight residual 180.00 159.82 20.18 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLU R 298 " pdb=" C GLU R 298 " pdb=" N ASN R 299 " pdb=" CA ASN R 299 " ideal model delta harmonic sigma weight residual 180.00 161.53 18.47 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 5448 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1300 0.092 - 0.184: 102 0.184 - 0.276: 3 0.276 - 0.369: 1 0.369 - 0.461: 2 Chirality restraints: 1408 Sorted by residual: chirality pdb=" CA SER A 44 " pdb=" N SER A 44 " pdb=" C SER A 44 " pdb=" CB SER A 44 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.31e+00 chirality pdb=" CA PRO L 3 " pdb=" N PRO L 3 " pdb=" C PRO L 3 " pdb=" CB PRO L 3 " both_signs ideal model delta sigma weight residual False 2.72 2.30 0.42 2.00e-01 2.50e+01 4.38e+00 chirality pdb=" CB VAL R 202 " pdb=" CA VAL R 202 " pdb=" CG1 VAL R 202 " pdb=" CG2 VAL R 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 1405 not shown) Planarity restraints: 1573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N PCA L 1 " -0.064 2.00e-02 2.50e+03 4.54e-02 2.58e+01 pdb=" CA PCA L 1 " 0.057 2.00e-02 2.50e+03 pdb=" CG PCA L 1 " -0.023 2.00e-02 2.50e+03 pdb=" CD PCA L 1 " -0.016 2.00e-02 2.50e+03 pdb=" OE PCA L 1 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 198 " 0.015 2.00e-02 2.50e+03 2.95e-02 8.69e+00 pdb=" C VAL R 198 " -0.051 2.00e-02 2.50e+03 pdb=" O VAL R 198 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE R 199 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 40 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C GLY A 40 " -0.039 2.00e-02 2.50e+03 pdb=" O GLY A 40 " 0.015 2.00e-02 2.50e+03 pdb=" N THR A 41 " 0.013 2.00e-02 2.50e+03 ... (remaining 1570 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 319 2.71 - 3.26: 8460 3.26 - 3.81: 14220 3.81 - 4.35: 18140 4.35 - 4.90: 31421 Nonbonded interactions: 72560 Sorted by model distance: nonbonded pdb=" OD1 ASP A 274 " pdb=" NZ LYS A 308 " model vdw 2.167 3.120 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.214 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.264 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.266 3.040 nonbonded pdb=" OE1 GLU A 234 " pdb=" NE2 HIS A 245 " model vdw 2.326 3.120 ... (remaining 72555 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: 0.480 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.700 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:5.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 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 : 0.005 0.104 9179 Z= 0.268 Angle : 0.682 14.803 12438 Z= 0.391 Chirality : 0.050 0.461 1408 Planarity : 0.005 0.064 1573 Dihedral : 12.265 77.123 3305 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.37 (0.25), residues: 1124 helix: 0.43 (0.26), residues: 384 sheet: 1.23 (0.32), residues: 272 loop : -0.41 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 22 TYR 0.021 0.002 TYR R 24 PHE 0.021 0.002 PHE R 161 TRP 0.020 0.001 TRP R 91 HIS 0.011 0.001 HIS L 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.25 ( 9176) covalent geometry : angle 0.68034 / 0.39 (12434) SS BOND : bond 0.00500 / 0.26 ( 2) SS BOND : angle 2.65471 / 1.53 ( 4) hydrogen bonds : bond 0.16642 / 11.59 ( 453) hydrogen bonds : angle 6.83606 / 5.05 ( 1272) Misc. bond : bond 0.08909 / 4.69 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.299 Fit side-chains REVERT: R 139 PHE cc_start: 0.8130 (t80) cc_final: 0.7129 (t80) REVERT: R 147 ILE cc_start: 0.8123 (pt) cc_final: 0.7897 (mt) REVERT: A 32 ARG cc_start: 0.6777 (mmt90) cc_final: 0.6502 (mmt90) REVERT: A 314 GLU cc_start: 0.6772 (mp0) cc_final: 0.6408 (mp0) REVERT: A 329 GLU cc_start: 0.6658 (mp0) cc_final: 0.6429 (mp0) REVERT: A 396 ASP cc_start: 0.6708 (m-30) cc_final: 0.6473 (m-30) REVERT: B 175 GLN cc_start: 0.7519 (mm-40) cc_final: 0.7294 (mm-40) REVERT: B 258 ASP cc_start: 0.6670 (t70) cc_final: 0.6390 (t70) REVERT: S 57 THR cc_start: 0.8332 (p) cc_final: 0.8104 (t) outliers start: 0 outliers final: 1 residues processed: 242 average time/residue: 0.4479 time to fit residues: 115.6694 Evaluate side-chains 227 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.0170 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 61 ASN A 400 GLN A 402 ASN B 176 GLN B 259 GLN B 293 ASN B 340 ASN S 167 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.132968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.115943 restraints weight = 11874.319| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.75 r_work: 0.3379 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9179 Z= 0.127 Angle : 0.568 9.907 12438 Z= 0.302 Chirality : 0.043 0.197 1408 Planarity : 0.004 0.049 1573 Dihedral : 4.497 37.588 1254 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.94 % Allowed : 8.06 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.26), residues: 1124 helix: 1.52 (0.26), residues: 383 sheet: 1.21 (0.31), residues: 309 loop : -0.31 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 22 TYR 0.015 0.001 TYR R 24 PHE 0.019 0.001 PHE R 161 TRP 0.015 0.001 TRP B 297 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 9176) covalent geometry : angle 0.56735 / 0.30 (12434) SS BOND : bond 0.00340 / 0.17 ( 2) SS BOND : angle 1.75671 / 1.00 ( 4) hydrogen bonds : bond 0.04405 / 3.10 ( 453) hydrogen bonds : angle 5.09338 / 3.74 ( 1272) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 226 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: R 141 ARG cc_start: 0.8063 (ttt-90) cc_final: 0.7825 (ttt180) REVERT: R 146 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8171 (mp) REVERT: R 147 ILE cc_start: 0.8253 (pt) cc_final: 0.8005 (mt) REVERT: R 202 VAL cc_start: 0.8214 (OUTLIER) cc_final: 0.7986 (t) REVERT: R 315 ILE cc_start: 0.8408 (mt) cc_final: 0.8187 (mp) REVERT: A 243 ASN cc_start: 0.8823 (m-40) cc_final: 0.8425 (m110) REVERT: A 329 GLU cc_start: 0.7165 (mp0) cc_final: 0.6847 (mp0) REVERT: A 375 TYR cc_start: 0.8577 (m-80) cc_final: 0.8323 (m-80) REVERT: A 396 ASP cc_start: 0.7512 (m-30) cc_final: 0.7239 (m-30) REVERT: B 175 GLN cc_start: 0.8116 (mm-40) cc_final: 0.7883 (mm-40) REVERT: B 258 ASP cc_start: 0.7345 (t70) cc_final: 0.6966 (t70) REVERT: S 128 MET cc_start: 0.8532 (mmm) cc_final: 0.8257 (mmm) outliers start: 19 outliers final: 7 residues processed: 235 average time/residue: 0.4757 time to fit residues: 118.8742 Evaluate side-chains 222 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 213 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 89 optimal weight: 0.0170 overall best weight: 1.0022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 400 GLN A 402 ASN B 259 GLN B 293 ASN B 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.131527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.114651 restraints weight = 11817.736| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.72 r_work: 0.3356 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9179 Z= 0.155 Angle : 0.571 10.943 12438 Z= 0.302 Chirality : 0.043 0.198 1408 Planarity : 0.004 0.048 1573 Dihedral : 4.642 44.737 1254 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.76 % Allowed : 11.02 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.20 (0.26), residues: 1124 helix: 1.79 (0.27), residues: 383 sheet: 1.22 (0.31), residues: 298 loop : -0.35 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 19 TYR 0.013 0.002 TYR S 178 PHE 0.013 0.001 PHE R 296 TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 9176) covalent geometry : angle 0.56995 / 0.30 (12434) SS BOND : bond 0.00337 / 0.17 ( 2) SS BOND : angle 1.67331 / 0.95 ( 4) hydrogen bonds : bond 0.04521 / 3.18 ( 453) hydrogen bonds : angle 4.96068 / 3.65 ( 1272) Misc. bond : bond 0.00069 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 217 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: R 146 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8167 (mp) REVERT: R 147 ILE cc_start: 0.8280 (pt) cc_final: 0.8024 (mt) REVERT: R 202 VAL cc_start: 0.8224 (OUTLIER) cc_final: 0.7991 (t) REVERT: R 315 ILE cc_start: 0.8399 (mt) cc_final: 0.8188 (mp) REVERT: A 243 ASN cc_start: 0.8765 (m-40) cc_final: 0.8370 (m-40) REVERT: A 273 VAL cc_start: 0.8831 (t) cc_final: 0.8625 (p) REVERT: A 329 GLU cc_start: 0.7200 (mp0) cc_final: 0.6667 (mp0) REVERT: A 375 TYR cc_start: 0.8596 (m-80) cc_final: 0.8321 (m-80) REVERT: A 389 ARG cc_start: 0.8248 (mtm180) cc_final: 0.8026 (mtm180) REVERT: A 396 ASP cc_start: 0.7539 (m-30) cc_final: 0.7235 (m-30) REVERT: B 175 GLN cc_start: 0.8086 (mm-40) cc_final: 0.7875 (mm-40) REVERT: B 258 ASP cc_start: 0.7376 (t70) cc_final: 0.6938 (t70) REVERT: S 18 ARG cc_start: 0.8113 (ttm-80) cc_final: 0.7819 (ttt180) REVERT: S 67 ARG cc_start: 0.8162 (ptm-80) cc_final: 0.7822 (ptm-80) REVERT: S 128 MET cc_start: 0.8527 (mmm) cc_final: 0.8225 (mmm) outliers start: 27 outliers final: 15 residues processed: 230 average time/residue: 0.4832 time to fit residues: 118.0393 Evaluate side-chains 228 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 211 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 177 ILE Chi-restraints excluded: chain R residue 179 CYS Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 98 optimal weight: 0.2980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 400 GLN A 402 ASN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.131561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.114232 restraints weight = 12012.258| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.78 r_work: 0.3342 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9179 Z= 0.156 Angle : 0.567 11.110 12438 Z= 0.301 Chirality : 0.043 0.197 1408 Planarity : 0.004 0.047 1573 Dihedral : 4.627 42.577 1254 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.45 % Allowed : 13.37 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.21 (0.26), residues: 1124 helix: 1.90 (0.27), residues: 383 sheet: 1.13 (0.31), residues: 297 loop : -0.37 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 22 TYR 0.016 0.002 TYR B 105 PHE 0.016 0.001 PHE R 139 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 9176) covalent geometry : angle 0.56619 / 0.30 (12434) SS BOND : bond 0.00410 / 0.21 ( 2) SS BOND : angle 1.61367 / 0.93 ( 4) hydrogen bonds : bond 0.04389 / 3.08 ( 453) hydrogen bonds : angle 4.91934 / 3.63 ( 1272) Misc. bond : bond 0.00077 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 215 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: R 146 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8199 (mp) REVERT: R 147 ILE cc_start: 0.8308 (pt) cc_final: 0.8044 (mt) REVERT: R 202 VAL cc_start: 0.8221 (OUTLIER) cc_final: 0.7985 (t) REVERT: A 243 ASN cc_start: 0.8795 (m-40) cc_final: 0.8438 (m-40) REVERT: A 273 VAL cc_start: 0.8797 (t) cc_final: 0.8587 (p) REVERT: A 329 GLU cc_start: 0.7175 (mp0) cc_final: 0.6637 (mp0) REVERT: A 375 TYR cc_start: 0.8626 (m-80) cc_final: 0.8322 (m-80) REVERT: A 396 ASP cc_start: 0.7587 (m-30) cc_final: 0.7277 (m-30) REVERT: B 45 MET cc_start: 0.8692 (mtt) cc_final: 0.8452 (mtm) REVERT: B 175 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7944 (mm-40) REVERT: B 258 ASP cc_start: 0.7476 (t70) cc_final: 0.6991 (t0) REVERT: S 67 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7732 (ptm-80) REVERT: S 128 MET cc_start: 0.8553 (mmm) cc_final: 0.8305 (mmm) outliers start: 24 outliers final: 18 residues processed: 226 average time/residue: 0.5140 time to fit residues: 123.2367 Evaluate side-chains 229 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 208 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 177 ILE Chi-restraints excluded: chain R residue 179 CYS Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 37 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 89 optimal weight: 0.0470 chunk 31 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 293 ASN A 400 GLN B 259 GLN B 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.132910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.115555 restraints weight = 11963.420| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.78 r_work: 0.3359 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9179 Z= 0.122 Angle : 0.539 10.828 12438 Z= 0.285 Chirality : 0.042 0.190 1408 Planarity : 0.004 0.043 1573 Dihedral : 4.481 42.748 1254 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.96 % Allowed : 14.29 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.26), residues: 1124 helix: 2.03 (0.27), residues: 384 sheet: 1.05 (0.31), residues: 299 loop : -0.31 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 22 TYR 0.019 0.001 TYR S 101 PHE 0.012 0.001 PHE R 296 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 9176) covalent geometry : angle 0.53802 / 0.29 (12434) SS BOND : bond 0.00302 / 0.15 ( 2) SS BOND : angle 1.44881 / 0.83 ( 4) hydrogen bonds : bond 0.04003 / 2.81 ( 453) hydrogen bonds : angle 4.81151 / 3.57 ( 1272) Misc. bond : bond 0.00054 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 216 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: R 147 ILE cc_start: 0.8297 (pt) cc_final: 0.8040 (mt) REVERT: R 202 VAL cc_start: 0.8197 (OUTLIER) cc_final: 0.7971 (t) REVERT: R 315 ILE cc_start: 0.8397 (mt) cc_final: 0.8188 (mp) REVERT: A 8 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7179 (mt-10) REVERT: A 243 ASN cc_start: 0.8781 (m-40) cc_final: 0.8408 (m-40) REVERT: A 329 GLU cc_start: 0.7173 (mp0) cc_final: 0.6826 (mp0) REVERT: A 375 TYR cc_start: 0.8630 (m-80) cc_final: 0.8310 (m-80) REVERT: A 396 ASP cc_start: 0.7579 (m-30) cc_final: 0.7270 (m-30) REVERT: B 45 MET cc_start: 0.8691 (mtt) cc_final: 0.8454 (mtm) REVERT: B 175 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7958 (mm-40) REVERT: B 184 THR cc_start: 0.8299 (p) cc_final: 0.7986 (m) REVERT: B 212 ASP cc_start: 0.8228 (p0) cc_final: 0.7874 (p0) REVERT: B 258 ASP cc_start: 0.7480 (t70) cc_final: 0.7272 (t70) REVERT: S 18 ARG cc_start: 0.7970 (ttm-80) cc_final: 0.7720 (ttt180) REVERT: S 67 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7777 (ptm-80) outliers start: 29 outliers final: 17 residues processed: 227 average time/residue: 0.5082 time to fit residues: 122.6366 Evaluate side-chains 227 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 208 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 177 ILE Chi-restraints excluded: chain R residue 179 CYS Chi-restraints excluded: chain R residue 198 VAL Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 105 optimal weight: 0.8980 chunk 43 optimal weight: 0.0010 chunk 84 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 259 GLN B 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.132957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.115567 restraints weight = 11991.492| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.79 r_work: 0.3364 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9179 Z= 0.119 Angle : 0.534 10.861 12438 Z= 0.283 Chirality : 0.042 0.190 1408 Planarity : 0.004 0.041 1573 Dihedral : 4.397 42.417 1252 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.96 % Allowed : 15.31 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.33 (0.26), residues: 1124 helix: 2.14 (0.27), residues: 384 sheet: 1.06 (0.31), residues: 292 loop : -0.32 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 404 TYR 0.020 0.001 TYR S 101 PHE 0.011 0.001 PHE R 296 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 9176) covalent geometry : angle 0.53380 / 0.28 (12434) SS BOND : bond 0.00305 / 0.15 ( 2) SS BOND : angle 1.38192 / 0.80 ( 4) hydrogen bonds : bond 0.03913 / 2.74 ( 453) hydrogen bonds : angle 4.77622 / 3.56 ( 1272) Misc. bond : bond 0.00047 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 216 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 30 LEU cc_start: 0.7573 (mt) cc_final: 0.7301 (mm) REVERT: R 147 ILE cc_start: 0.8277 (pt) cc_final: 0.7976 (mp) REVERT: R 176 VAL cc_start: 0.7488 (t) cc_final: 0.7045 (p) REVERT: R 202 VAL cc_start: 0.8207 (OUTLIER) cc_final: 0.7984 (t) REVERT: A 329 GLU cc_start: 0.7160 (mp0) cc_final: 0.6816 (mp0) REVERT: A 375 TYR cc_start: 0.8625 (m-80) cc_final: 0.8310 (m-80) REVERT: A 396 ASP cc_start: 0.7584 (m-30) cc_final: 0.7279 (m-30) REVERT: B 45 MET cc_start: 0.8683 (mtt) cc_final: 0.8439 (mtm) REVERT: B 175 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7962 (mm-40) REVERT: B 184 THR cc_start: 0.8258 (p) cc_final: 0.7970 (m) REVERT: B 212 ASP cc_start: 0.8180 (p0) cc_final: 0.7827 (p0) REVERT: B 258 ASP cc_start: 0.7373 (t70) cc_final: 0.7128 (t70) REVERT: S 18 ARG cc_start: 0.7948 (ttm-80) cc_final: 0.7696 (ttt180) REVERT: S 67 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7815 (ptm-80) REVERT: S 167 GLN cc_start: 0.8573 (tt0) cc_final: 0.8331 (tt0) outliers start: 29 outliers final: 20 residues processed: 227 average time/residue: 0.5034 time to fit residues: 121.4307 Evaluate side-chains 234 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 212 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 177 ILE Chi-restraints excluded: chain R residue 179 CYS Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 17 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 chunk 7 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 25 GLN B 259 GLN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.131241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.113837 restraints weight = 11996.225| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.78 r_work: 0.3337 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9179 Z= 0.171 Angle : 0.578 10.871 12438 Z= 0.309 Chirality : 0.044 0.206 1408 Planarity : 0.004 0.042 1573 Dihedral : 4.583 42.626 1252 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.57 % Allowed : 15.10 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.21 (0.26), residues: 1124 helix: 1.99 (0.27), residues: 385 sheet: 0.99 (0.30), residues: 302 loop : -0.39 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 123 TYR 0.012 0.002 TYR S 178 PHE 0.012 0.001 PHE R 296 TRP 0.015 0.002 TRP B 82 HIS 0.005 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 ( 9176) covalent geometry : angle 0.57749 / 0.31 (12434) SS BOND : bond 0.00528 / 0.27 ( 2) SS BOND : angle 1.49958 / 0.86 ( 4) hydrogen bonds : bond 0.04496 / 3.15 ( 453) hydrogen bonds : angle 4.92063 / 3.66 ( 1272) Misc. bond : bond 0.00051 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 210 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: R 30 LEU cc_start: 0.7585 (mt) cc_final: 0.7378 (mm) REVERT: R 122 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7566 (mt-10) REVERT: R 147 ILE cc_start: 0.8314 (pt) cc_final: 0.8086 (mt) REVERT: R 202 VAL cc_start: 0.8277 (OUTLIER) cc_final: 0.8044 (t) REVERT: A 329 GLU cc_start: 0.7184 (mp0) cc_final: 0.6845 (mp0) REVERT: A 375 TYR cc_start: 0.8627 (m-80) cc_final: 0.8301 (m-80) REVERT: A 379 THR cc_start: 0.8367 (p) cc_final: 0.8103 (m) REVERT: A 396 ASP cc_start: 0.7621 (m-30) cc_final: 0.7301 (m-30) REVERT: B 45 MET cc_start: 0.8696 (mtt) cc_final: 0.8456 (mtm) REVERT: B 175 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7971 (mm-40) REVERT: B 184 THR cc_start: 0.8324 (p) cc_final: 0.8035 (m) REVERT: B 212 ASP cc_start: 0.8178 (p0) cc_final: 0.7828 (p0) REVERT: B 258 ASP cc_start: 0.7405 (t70) cc_final: 0.7157 (t70) REVERT: S 67 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7955 (ptm-80) REVERT: S 167 GLN cc_start: 0.8584 (tt0) cc_final: 0.8326 (tt0) outliers start: 35 outliers final: 22 residues processed: 226 average time/residue: 0.5832 time to fit residues: 140.0450 Evaluate side-chains 231 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 177 ILE Chi-restraints excluded: chain R residue 179 CYS Chi-restraints excluded: chain R residue 198 VAL Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 72 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.2980 chunk 65 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 25 GLN A 245 HIS A 400 GLN B 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.131659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.114270 restraints weight = 11998.412| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.79 r_work: 0.3349 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9179 Z= 0.156 Angle : 0.574 10.989 12438 Z= 0.304 Chirality : 0.043 0.203 1408 Planarity : 0.004 0.042 1573 Dihedral : 4.533 41.218 1252 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.16 % Allowed : 15.92 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.26), residues: 1124 helix: 1.98 (0.27), residues: 385 sheet: 0.98 (0.30), residues: 303 loop : -0.42 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 314 TYR 0.012 0.002 TYR S 178 PHE 0.016 0.001 PHE R 304 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 9176) covalent geometry : angle 0.57391 / 0.30 (12434) SS BOND : bond 0.00443 / 0.23 ( 2) SS BOND : angle 1.48516 / 0.86 ( 4) hydrogen bonds : bond 0.04298 / 3.01 ( 453) hydrogen bonds : angle 4.89220 / 3.64 ( 1272) Misc. bond : bond 0.00051 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: R 122 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7565 (mt-10) REVERT: R 147 ILE cc_start: 0.8310 (pt) cc_final: 0.8080 (mt) REVERT: R 202 VAL cc_start: 0.8284 (OUTLIER) cc_final: 0.8062 (t) REVERT: A 8 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7317 (mt-10) REVERT: A 329 GLU cc_start: 0.7211 (mp0) cc_final: 0.6860 (mp0) REVERT: A 375 TYR cc_start: 0.8637 (m-80) cc_final: 0.8323 (m-80) REVERT: A 379 THR cc_start: 0.8363 (p) cc_final: 0.8117 (m) REVERT: A 396 ASP cc_start: 0.7631 (m-30) cc_final: 0.7308 (m-30) REVERT: B 45 MET cc_start: 0.8697 (mtt) cc_final: 0.8456 (mtm) REVERT: B 175 GLN cc_start: 0.8209 (mm-40) cc_final: 0.8007 (mm-40) REVERT: B 184 THR cc_start: 0.8336 (p) cc_final: 0.8050 (m) REVERT: S 167 GLN cc_start: 0.8588 (tt0) cc_final: 0.8320 (tt0) outliers start: 31 outliers final: 25 residues processed: 216 average time/residue: 0.5668 time to fit residues: 130.0550 Evaluate side-chains 230 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 177 ILE Chi-restraints excluded: chain R residue 179 CYS Chi-restraints excluded: chain R residue 198 VAL Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 15 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 11 optimal weight: 0.3980 chunk 75 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 HIS A 400 GLN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.131612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.114261 restraints weight = 11919.225| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.77 r_work: 0.3343 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9179 Z= 0.161 Angle : 0.586 12.338 12438 Z= 0.310 Chirality : 0.044 0.206 1408 Planarity : 0.004 0.041 1573 Dihedral : 4.543 41.288 1252 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.27 % Allowed : 16.22 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1124 helix: 1.98 (0.27), residues: 385 sheet: 0.95 (0.30), residues: 303 loop : -0.45 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 314 TYR 0.013 0.002 TYR S 178 PHE 0.014 0.001 PHE R 304 TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 9176) covalent geometry : angle 0.58519 / 0.31 (12434) SS BOND : bond 0.00481 / 0.24 ( 2) SS BOND : angle 1.50537 / 0.87 ( 4) hydrogen bonds : bond 0.04342 / 3.05 ( 453) hydrogen bonds : angle 4.91332 / 3.65 ( 1272) Misc. bond : bond 0.00052 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: R 122 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7568 (mt-10) REVERT: R 147 ILE cc_start: 0.8307 (pt) cc_final: 0.8089 (mt) REVERT: R 158 MET cc_start: 0.6709 (mtp) cc_final: 0.6465 (mtp) REVERT: R 202 VAL cc_start: 0.8281 (OUTLIER) cc_final: 0.8066 (t) REVERT: A 8 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7327 (mt-10) REVERT: A 329 GLU cc_start: 0.7200 (mp0) cc_final: 0.6846 (mp0) REVERT: A 375 TYR cc_start: 0.8624 (m-80) cc_final: 0.8304 (m-80) REVERT: A 379 THR cc_start: 0.8364 (p) cc_final: 0.8122 (m) REVERT: A 396 ASP cc_start: 0.7608 (m-30) cc_final: 0.7289 (m-30) REVERT: B 45 MET cc_start: 0.8693 (mtt) cc_final: 0.8453 (mtm) REVERT: B 184 THR cc_start: 0.8309 (p) cc_final: 0.8035 (m) REVERT: B 258 ASP cc_start: 0.7407 (t70) cc_final: 0.6959 (t70) REVERT: S 167 GLN cc_start: 0.8587 (tt0) cc_final: 0.8312 (tt0) outliers start: 32 outliers final: 27 residues processed: 224 average time/residue: 0.5813 time to fit residues: 138.2475 Evaluate side-chains 233 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 GLU Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 141 ARG Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 177 ILE Chi-restraints excluded: chain R residue 179 CYS Chi-restraints excluded: chain R residue 198 VAL Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 77 optimal weight: 1.9990 chunk 40 optimal weight: 0.0970 chunk 66 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 400 GLN B 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.131948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.114569 restraints weight = 11904.665| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.78 r_work: 0.3348 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9179 Z= 0.150 Angle : 0.586 11.489 12438 Z= 0.308 Chirality : 0.044 0.234 1408 Planarity : 0.004 0.041 1573 Dihedral : 4.518 40.880 1252 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.37 % Allowed : 16.33 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.17 (0.26), residues: 1124 helix: 2.00 (0.27), residues: 385 sheet: 0.95 (0.30), residues: 303 loop : -0.44 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 314 TYR 0.013 0.001 TYR R 24 PHE 0.015 0.001 PHE R 304 TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 9176) covalent geometry : angle 0.58535 / 0.31 (12434) SS BOND : bond 0.00447 / 0.22 ( 2) SS BOND : angle 1.46275 / 0.84 ( 4) hydrogen bonds : bond 0.04249 / 2.99 ( 453) hydrogen bonds : angle 4.93295 / 3.68 ( 1272) Misc. bond : bond 0.00047 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 208 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: R 122 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7575 (mt-10) REVERT: R 147 ILE cc_start: 0.8301 (pt) cc_final: 0.8093 (mt) REVERT: R 158 MET cc_start: 0.6668 (mtp) cc_final: 0.6441 (mtp) REVERT: A 8 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7298 (mt-10) REVERT: A 329 GLU cc_start: 0.7199 (mp0) cc_final: 0.6848 (mp0) REVERT: A 375 TYR cc_start: 0.8629 (m-80) cc_final: 0.8315 (m-80) REVERT: A 379 THR cc_start: 0.8331 (p) cc_final: 0.8119 (m) REVERT: A 396 ASP cc_start: 0.7614 (m-30) cc_final: 0.7289 (m-30) REVERT: B 45 MET cc_start: 0.8694 (mtt) cc_final: 0.8452 (mtm) REVERT: B 184 THR cc_start: 0.8300 (p) cc_final: 0.8014 (m) REVERT: B 212 ASP cc_start: 0.8169 (p0) cc_final: 0.7798 (p0) REVERT: B 258 ASP cc_start: 0.7389 (t70) cc_final: 0.6966 (t70) REVERT: S 167 GLN cc_start: 0.8589 (tt0) cc_final: 0.8311 (tt0) outliers start: 33 outliers final: 27 residues processed: 223 average time/residue: 0.5181 time to fit residues: 123.0016 Evaluate side-chains 233 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 205 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 GLU Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 177 ILE Chi-restraints excluded: chain R residue 179 CYS Chi-restraints excluded: chain R residue 198 VAL Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 23 optimal weight: 0.4980 chunk 71 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 87 optimal weight: 0.0770 chunk 16 optimal weight: 4.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 HIS A 400 GLN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.133080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.115788 restraints weight = 11778.641| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.76 r_work: 0.3366 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9179 Z= 0.126 Angle : 0.571 11.860 12438 Z= 0.296 Chirality : 0.044 0.409 1408 Planarity : 0.004 0.040 1573 Dihedral : 4.396 40.465 1252 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.06 % Allowed : 17.24 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.26), residues: 1124 helix: 2.20 (0.27), residues: 379 sheet: 0.97 (0.30), residues: 301 loop : -0.42 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 314 TYR 0.013 0.001 TYR S 178 PHE 0.014 0.001 PHE R 304 TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 9176) covalent geometry : angle 0.57023 / 0.30 (12434) SS BOND : bond 0.00396 / 0.19 ( 2) SS BOND : angle 1.40302 / 0.80 ( 4) hydrogen bonds : bond 0.03949 / 2.79 ( 453) hydrogen bonds : angle 4.85409 / 3.63 ( 1272) Misc. bond : bond 0.00034 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3356.34 seconds wall clock time: 57 minutes 41.95 seconds (3461.95 seconds total)