Starting phenix.real_space_refine on Sat Jul 26 20:40:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xw9_33494/07_2025/7xw9_33494.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xw9_33494/07_2025/7xw9_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xw9_33494/07_2025/7xw9_33494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xw9_33494/07_2025/7xw9_33494.map" model { file = "/net/cci-nas-00/data/ceres_data/7xw9_33494/07_2025/7xw9_33494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xw9_33494/07_2025/7xw9_33494.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.51, per 1000 atoms: 0.61 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: 2.36 Conformation dependent library (CDL) restraints added in 944.7 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: 0.92 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: 2.43 Time building geometry restraints manager: 2.78 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: 0.300 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.970 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.020 0.001 TRP R 91 HIS 0.011 0.001 HIS L 2 PHE 0.021 0.002 PHE R 161 TYR 0.021 0.002 TYR R 24 ARG 0.016 0.001 ARG B 22 Details of bonding type rmsd hydrogen bonds : bond 0.16642 ( 453) hydrogen bonds : angle 6.83606 ( 1272) SS BOND : bond 0.00500 ( 2) SS BOND : angle 2.65471 ( 4) covalent geometry : bond 0.00531 ( 9176) covalent geometry : angle 0.68034 (12434) Misc. bond : bond 0.08909 ( 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 : 1.021 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: 1.1805 time to fit residues: 304.8819 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 : 0.938 ------------------------------------------------------------------------------- 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 93 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.0170 chunk 52 optimal weight: 0.0050 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.9836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3708 r_free = 0.3708 target = 0.131742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.114624 restraints weight = 11728.684| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.74 r_work: 0.3357 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9179 Z= 0.159 Angle : 0.589 9.846 12438 Z= 0.314 Chirality : 0.044 0.204 1408 Planarity : 0.004 0.051 1573 Dihedral : 4.644 37.580 1254 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.14 % Allowed : 7.96 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.26), residues: 1124 helix: 1.43 (0.26), residues: 383 sheet: 1.22 (0.31), residues: 304 loop : -0.35 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.005 0.001 HIS B 62 PHE 0.017 0.001 PHE R 161 TYR 0.014 0.002 TYR R 24 ARG 0.008 0.001 ARG B 22 Details of bonding type rmsd hydrogen bonds : bond 0.04851 ( 453) hydrogen bonds : angle 5.15037 ( 1272) SS BOND : bond 0.00479 ( 2) SS BOND : angle 1.95914 ( 4) covalent geometry : bond 0.00365 ( 9176) covalent geometry : angle 0.58842 (12434) Misc. bond : bond 0.00078 ( 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 242 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 221 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: R 141 ARG cc_start: 0.8108 (ttt-90) cc_final: 0.7880 (ttt180) REVERT: R 146 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8172 (mp) REVERT: R 147 ILE cc_start: 0.8266 (pt) cc_final: 0.8021 (mt) REVERT: R 202 VAL cc_start: 0.8247 (OUTLIER) cc_final: 0.8004 (t) REVERT: R 315 ILE cc_start: 0.8408 (mt) cc_final: 0.8190 (mp) REVERT: A 243 ASN cc_start: 0.8838 (m-40) cc_final: 0.8431 (m110) REVERT: A 329 GLU cc_start: 0.7190 (mp0) cc_final: 0.6695 (mp0) REVERT: A 375 TYR cc_start: 0.8588 (m-80) cc_final: 0.8302 (m-80) REVERT: A 396 ASP cc_start: 0.7527 (m-30) cc_final: 0.7249 (m-30) REVERT: B 22 ARG cc_start: 0.7364 (mtt90) cc_final: 0.6830 (mpt180) REVERT: B 175 GLN cc_start: 0.8110 (mm-40) cc_final: 0.7876 (mm-40) REVERT: B 258 ASP cc_start: 0.7364 (t70) cc_final: 0.6312 (t70) outliers start: 21 outliers final: 6 residues processed: 230 average time/residue: 1.3683 time to fit residues: 333.0898 Evaluate side-chains 222 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 214 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 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 10 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN A 400 GLN B 259 GLN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.131447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.114422 restraints weight = 11989.894| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.76 r_work: 0.3347 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1482 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= 0.152 Angle : 0.576 10.765 12438 Z= 0.303 Chirality : 0.044 0.199 1408 Planarity : 0.004 0.048 1573 Dihedral : 4.661 45.776 1254 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.86 % Allowed : 11.02 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.26), residues: 1124 helix: 1.75 (0.27), residues: 383 sheet: 1.18 (0.31), residues: 298 loop : -0.41 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS L 2 PHE 0.017 0.001 PHE R 139 TYR 0.013 0.002 TYR S 178 ARG 0.008 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 453) hydrogen bonds : angle 4.95868 ( 1272) SS BOND : bond 0.00468 ( 2) SS BOND : angle 1.88655 ( 4) covalent geometry : bond 0.00351 ( 9176) covalent geometry : angle 0.57501 (12434) Misc. bond : bond 0.00096 ( 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 247 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 219 time to evaluate : 1.400 Fit side-chains revert: symmetry clash REVERT: R 146 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8149 (mp) REVERT: R 147 ILE cc_start: 0.8269 (pt) cc_final: 0.8019 (mt) REVERT: R 202 VAL cc_start: 0.8248 (OUTLIER) cc_final: 0.8010 (t) REVERT: R 315 ILE cc_start: 0.8404 (mt) cc_final: 0.8191 (mp) REVERT: A 243 ASN cc_start: 0.8786 (m-40) cc_final: 0.8385 (m-40) REVERT: A 273 VAL cc_start: 0.8815 (t) cc_final: 0.8612 (p) REVERT: A 329 GLU cc_start: 0.7212 (mp0) cc_final: 0.6671 (mp0) REVERT: A 375 TYR cc_start: 0.8610 (m-80) cc_final: 0.8338 (m-80) REVERT: A 389 ARG cc_start: 0.8239 (mtm180) cc_final: 0.8015 (mtm180) REVERT: A 396 ASP cc_start: 0.7564 (m-30) cc_final: 0.7262 (m-30) REVERT: B 45 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.7961 (mtm) REVERT: B 175 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7891 (mm-40) REVERT: B 258 ASP cc_start: 0.7397 (t70) cc_final: 0.6909 (t70) REVERT: S 18 ARG cc_start: 0.8130 (ttm-80) cc_final: 0.7781 (ttt180) outliers start: 28 outliers final: 17 residues processed: 230 average time/residue: 1.6439 time to fit residues: 401.7392 Evaluate side-chains 230 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 210 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 SER 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 43 ILE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 48 ARG 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 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 54 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 GLN B 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.129305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.112020 restraints weight = 11838.858| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.75 r_work: 0.3315 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 9179 Z= 0.259 Angle : 0.651 11.688 12438 Z= 0.346 Chirality : 0.047 0.220 1408 Planarity : 0.005 0.053 1573 Dihedral : 5.074 48.465 1254 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.86 % Allowed : 13.57 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.26), residues: 1124 helix: 1.61 (0.27), residues: 383 sheet: 1.06 (0.31), residues: 308 loop : -0.53 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.008 0.002 HIS B 62 PHE 0.017 0.002 PHE R 296 TYR 0.023 0.002 TYR B 105 ARG 0.009 0.001 ARG B 22 Details of bonding type rmsd hydrogen bonds : bond 0.05391 ( 453) hydrogen bonds : angle 5.16485 ( 1272) SS BOND : bond 0.00950 ( 2) SS BOND : angle 1.94463 ( 4) covalent geometry : bond 0.00623 ( 9176) covalent geometry : angle 0.64995 (12434) Misc. bond : bond 0.00108 ( 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 245 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 217 time to evaluate : 1.053 Fit side-chains revert: symmetry clash REVERT: R 146 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8206 (mp) REVERT: R 147 ILE cc_start: 0.8310 (pt) cc_final: 0.8071 (mt) REVERT: A 8 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7418 (mt-10) REVERT: A 243 ASN cc_start: 0.8820 (m-40) cc_final: 0.8374 (m110) REVERT: A 329 GLU cc_start: 0.7284 (mp0) cc_final: 0.6930 (mp0) REVERT: A 375 TYR cc_start: 0.8621 (m-80) cc_final: 0.8329 (m-80) REVERT: A 389 ARG cc_start: 0.8215 (mtm180) cc_final: 0.7730 (mtt180) REVERT: A 396 ASP cc_start: 0.7646 (m-30) cc_final: 0.7352 (m-30) REVERT: B 22 ARG cc_start: 0.7573 (mtt90) cc_final: 0.7055 (mmm-85) REVERT: B 258 ASP cc_start: 0.7564 (t70) cc_final: 0.6821 (t0) REVERT: S 201 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.8102 (m) outliers start: 28 outliers final: 18 residues processed: 228 average time/residue: 1.6274 time to fit residues: 392.0740 Evaluate side-chains 233 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 213 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 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 18 MET Chi-restraints excluded: chain A residue 32 ARG 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 336 LEU 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 88 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 87 optimal weight: 0.3980 chunk 103 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.131936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.114705 restraints weight = 11830.373| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.76 r_work: 0.3352 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9179 Z= 0.128 Angle : 0.558 11.170 12438 Z= 0.295 Chirality : 0.043 0.203 1408 Planarity : 0.004 0.046 1573 Dihedral : 4.623 41.783 1254 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.86 % Allowed : 15.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.26), residues: 1124 helix: 1.89 (0.27), residues: 383 sheet: 1.04 (0.30), residues: 307 loop : -0.47 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS A 372 PHE 0.014 0.001 PHE R 139 TYR 0.014 0.001 TYR S 101 ARG 0.005 0.000 ARG B 22 Details of bonding type rmsd hydrogen bonds : bond 0.04181 ( 453) hydrogen bonds : angle 4.91724 ( 1272) SS BOND : bond 0.00378 ( 2) SS BOND : angle 1.62540 ( 4) covalent geometry : bond 0.00290 ( 9176) covalent geometry : angle 0.55763 (12434) Misc. bond : bond 0.00048 ( 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 244 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: R 122 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7502 (mt-10) REVERT: R 146 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8165 (mp) REVERT: R 147 ILE cc_start: 0.8296 (pt) cc_final: 0.8048 (mt) REVERT: R 202 VAL cc_start: 0.8252 (OUTLIER) cc_final: 0.8022 (t) REVERT: A 8 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7239 (mt-10) REVERT: A 46 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7741 (pttt) REVERT: A 243 ASN cc_start: 0.8797 (m-40) cc_final: 0.8438 (m-40) REVERT: A 329 GLU cc_start: 0.7238 (mp0) cc_final: 0.6884 (mp0) REVERT: A 375 TYR cc_start: 0.8644 (m-80) cc_final: 0.8324 (m-80) REVERT: A 396 ASP cc_start: 0.7624 (m-30) cc_final: 0.7311 (m-30) REVERT: B 175 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7949 (mm-40) REVERT: B 212 ASP cc_start: 0.8181 (p0) cc_final: 0.7804 (p0) REVERT: B 258 ASP cc_start: 0.7542 (t70) cc_final: 0.7048 (t0) REVERT: S 18 ARG cc_start: 0.8061 (ttm-80) cc_final: 0.7708 (ttt180) REVERT: S 167 GLN cc_start: 0.8559 (tt0) cc_final: 0.8335 (tt0) outliers start: 28 outliers final: 16 residues processed: 228 average time/residue: 1.3083 time to fit residues: 315.8863 Evaluate side-chains 229 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 210 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 SER Chi-restraints excluded: chain R residue 146 ILE 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 32 ARG Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP 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 62 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 43 optimal weight: 0.2980 chunk 90 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3710 r_free = 0.3710 target = 0.132031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.114707 restraints weight = 11881.962| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.78 r_work: 0.3349 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9179 Z= 0.129 Angle : 0.552 11.156 12438 Z= 0.291 Chirality : 0.043 0.203 1408 Planarity : 0.004 0.044 1573 Dihedral : 4.521 42.759 1252 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.37 % Allowed : 15.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.26), residues: 1124 helix: 2.07 (0.27), residues: 378 sheet: 0.97 (0.30), residues: 308 loop : -0.34 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.012 0.001 PHE R 296 TYR 0.020 0.001 TYR S 101 ARG 0.005 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04076 ( 453) hydrogen bonds : angle 4.86079 ( 1272) SS BOND : bond 0.00343 ( 2) SS BOND : angle 1.60864 ( 4) covalent geometry : bond 0.00295 ( 9176) covalent geometry : angle 0.55153 (12434) Misc. bond : bond 0.00051 ( 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 251 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 218 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: R 30 LEU cc_start: 0.7596 (mt) cc_final: 0.7315 (mm) REVERT: R 122 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7562 (mt-10) REVERT: R 146 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8189 (mp) REVERT: R 147 ILE cc_start: 0.8283 (pt) cc_final: 0.8022 (mt) REVERT: R 202 VAL cc_start: 0.8233 (OUTLIER) cc_final: 0.8020 (t) REVERT: A 243 ASN cc_start: 0.8796 (m-40) cc_final: 0.8423 (m-40) REVERT: A 329 GLU cc_start: 0.7216 (mp0) cc_final: 0.6864 (mp0) REVERT: A 375 TYR cc_start: 0.8642 (m-80) cc_final: 0.8321 (m-80) REVERT: A 396 ASP cc_start: 0.7613 (m-30) cc_final: 0.7302 (m-30) REVERT: B 45 MET cc_start: 0.8578 (mtm) cc_final: 0.8345 (mtt) REVERT: B 175 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7950 (mm-40) REVERT: B 188 MET cc_start: 0.8635 (mmm) cc_final: 0.8434 (mmt) REVERT: B 212 ASP cc_start: 0.8155 (p0) cc_final: 0.7797 (p0) REVERT: B 258 ASP cc_start: 0.7513 (t70) cc_final: 0.7038 (t0) REVERT: S 18 ARG cc_start: 0.8056 (ttm-80) cc_final: 0.7701 (ttt180) REVERT: S 167 GLN cc_start: 0.8567 (tt0) cc_final: 0.8329 (tt0) outliers start: 33 outliers final: 23 residues processed: 233 average time/residue: 1.2453 time to fit residues: 308.6968 Evaluate side-chains 233 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 208 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 146 ILE 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 32 ARG Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 306 LEU 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 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 B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 203 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 45 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3699 r_free = 0.3699 target = 0.131246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.113881 restraints weight = 11950.804| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.78 r_work: 0.3340 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9179 Z= 0.159 Angle : 0.573 11.165 12438 Z= 0.302 Chirality : 0.044 0.211 1408 Planarity : 0.004 0.046 1573 Dihedral : 4.615 42.584 1252 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.57 % Allowed : 16.33 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.26), residues: 1124 helix: 1.97 (0.27), residues: 379 sheet: 0.91 (0.30), residues: 308 loop : -0.37 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.012 0.001 PHE R 139 TYR 0.020 0.002 TYR S 101 ARG 0.004 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04380 ( 453) hydrogen bonds : angle 4.91223 ( 1272) SS BOND : bond 0.00502 ( 2) SS BOND : angle 1.68381 ( 4) covalent geometry : bond 0.00375 ( 9176) covalent geometry : angle 0.57244 (12434) Misc. bond : bond 0.00053 ( 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 243 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: R 30 LEU cc_start: 0.7607 (mt) cc_final: 0.7364 (mm) REVERT: R 122 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7553 (mt-10) REVERT: R 147 ILE cc_start: 0.8301 (pt) cc_final: 0.8041 (mt) REVERT: R 202 VAL cc_start: 0.8252 (OUTLIER) cc_final: 0.8050 (t) REVERT: A 329 GLU cc_start: 0.7231 (mp0) cc_final: 0.6877 (mp0) REVERT: A 375 TYR cc_start: 0.8643 (m-80) cc_final: 0.8349 (m-80) REVERT: A 379 THR cc_start: 0.8344 (p) cc_final: 0.8105 (m) REVERT: A 396 ASP cc_start: 0.7620 (m-30) cc_final: 0.7297 (m-30) REVERT: B 175 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7977 (mm-40) REVERT: B 188 MET cc_start: 0.8601 (mmm) cc_final: 0.8388 (mmt) REVERT: S 18 ARG cc_start: 0.8067 (ttm-80) cc_final: 0.7725 (ttt180) REVERT: S 167 GLN cc_start: 0.8588 (tt0) cc_final: 0.8324 (tt0) outliers start: 35 outliers final: 27 residues processed: 225 average time/residue: 1.3039 time to fit residues: 311.2684 Evaluate side-chains 235 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 206 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 32 ARG Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 306 LEU 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 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 336 LEU 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 90 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 42 optimal weight: 0.0980 chunk 82 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 48 optimal weight: 0.3980 chunk 60 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 297 GLN A 245 HIS A 400 GLN B 259 GLN B 293 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.132938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.115559 restraints weight = 12143.673| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.80 r_work: 0.3364 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9179 Z= 0.116 Angle : 0.542 11.200 12438 Z= 0.286 Chirality : 0.042 0.206 1408 Planarity : 0.004 0.041 1573 Dihedral : 4.396 39.292 1252 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.06 % Allowed : 17.35 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.26), residues: 1124 helix: 2.19 (0.27), residues: 378 sheet: 0.96 (0.30), residues: 301 loop : -0.41 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.014 0.001 PHE R 304 TYR 0.019 0.001 TYR S 101 ARG 0.006 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 453) hydrogen bonds : angle 4.79006 ( 1272) SS BOND : bond 0.00301 ( 2) SS BOND : angle 1.55180 ( 4) covalent geometry : bond 0.00260 ( 9176) covalent geometry : angle 0.54103 (12434) Misc. bond : bond 0.00031 ( 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 237 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: R 30 LEU cc_start: 0.7601 (mt) cc_final: 0.7387 (mm) REVERT: R 122 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7552 (mt-10) REVERT: R 147 ILE cc_start: 0.8302 (pt) cc_final: 0.8002 (mp) REVERT: A 329 GLU cc_start: 0.7217 (mp0) cc_final: 0.6876 (mp0) REVERT: A 375 TYR cc_start: 0.8637 (m-80) cc_final: 0.8330 (m-80) REVERT: A 379 THR cc_start: 0.8321 (p) cc_final: 0.8081 (m) REVERT: A 396 ASP cc_start: 0.7599 (m-30) cc_final: 0.7290 (m-30) REVERT: B 175 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7983 (mm-40) REVERT: B 184 THR cc_start: 0.8357 (p) cc_final: 0.8022 (m) REVERT: B 258 ASP cc_start: 0.7480 (t70) cc_final: 0.7105 (OUTLIER) REVERT: S 18 ARG cc_start: 0.8066 (ttm170) cc_final: 0.7714 (ttt180) REVERT: S 167 GLN cc_start: 0.8586 (tt0) cc_final: 0.8304 (tt0) outliers start: 30 outliers final: 23 residues processed: 221 average time/residue: 1.2792 time to fit residues: 300.6043 Evaluate side-chains 228 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 205 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 32 ARG 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 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 322 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 71 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3701 r_free = 0.3701 target = 0.131383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.113951 restraints weight = 11946.190| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.78 r_work: 0.3338 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2007 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= 0.169 Angle : 0.583 11.511 12438 Z= 0.306 Chirality : 0.043 0.143 1408 Planarity : 0.004 0.043 1573 Dihedral : 4.612 42.194 1252 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.86 % Allowed : 17.55 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.26), residues: 1124 helix: 2.03 (0.27), residues: 379 sheet: 0.91 (0.30), residues: 303 loop : -0.45 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.014 0.001 PHE R 304 TYR 0.012 0.002 TYR S 178 ARG 0.005 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.04375 ( 453) hydrogen bonds : angle 4.93907 ( 1272) SS BOND : bond 0.00524 ( 2) SS BOND : angle 1.66329 ( 4) covalent geometry : bond 0.00401 ( 9176) covalent geometry : angle 0.58194 (12434) Misc. bond : bond 0.00059 ( 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: 28 poor density : 211 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: R 30 LEU cc_start: 0.7580 (mt) cc_final: 0.7358 (mm) REVERT: R 122 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7568 (mt-10) REVERT: R 147 ILE cc_start: 0.8324 (pt) cc_final: 0.8081 (mt) REVERT: A 8 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7378 (mt-10) REVERT: A 329 GLU cc_start: 0.7210 (mp0) cc_final: 0.6862 (mp0) REVERT: A 375 TYR cc_start: 0.8628 (m-80) cc_final: 0.8320 (m-80) REVERT: A 379 THR cc_start: 0.8328 (p) cc_final: 0.8125 (m) REVERT: A 396 ASP cc_start: 0.7624 (m-30) cc_final: 0.7305 (m-30) REVERT: B 175 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7963 (mm-40) REVERT: B 212 ASP cc_start: 0.8115 (p0) cc_final: 0.7727 (p0) REVERT: B 258 ASP cc_start: 0.7462 (t70) cc_final: 0.7110 (t0) REVERT: S 18 ARG cc_start: 0.8060 (ttm170) cc_final: 0.7716 (ttt180) REVERT: S 167 GLN cc_start: 0.8590 (tt0) cc_final: 0.8313 (tt0) outliers start: 28 outliers final: 23 residues processed: 223 average time/residue: 1.3146 time to fit residues: 311.1590 Evaluate side-chains 233 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 209 time to evaluate : 1.490 ------------------------------------------------------------------------------- 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 R residue 280 MET Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 245 HIS 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 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 192 SER Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 59 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 21 optimal weight: 0.0050 chunk 80 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 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 = 0.3690 r_free = 0.3690 target = 0.130573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.113153 restraints weight = 11973.746| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.77 r_work: 0.3323 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 9179 Z= 0.197 Angle : 0.608 11.882 12438 Z= 0.320 Chirality : 0.045 0.154 1408 Planarity : 0.004 0.046 1573 Dihedral : 4.745 43.250 1252 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.86 % Allowed : 17.55 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.26), residues: 1124 helix: 1.86 (0.27), residues: 385 sheet: 0.91 (0.30), residues: 304 loop : -0.50 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.018 0.002 PHE R 304 TYR 0.013 0.002 TYR S 178 ARG 0.005 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.04650 ( 453) hydrogen bonds : angle 5.01744 ( 1272) SS BOND : bond 0.00671 ( 2) SS BOND : angle 1.70441 ( 4) covalent geometry : bond 0.00472 ( 9176) covalent geometry : angle 0.60684 (12434) Misc. bond : bond 0.00075 ( 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 242 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: R 30 LEU cc_start: 0.7603 (mt) cc_final: 0.7399 (mm) REVERT: R 122 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7569 (mt-10) REVERT: R 147 ILE cc_start: 0.8340 (pt) cc_final: 0.8103 (mt) REVERT: A 8 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7392 (mt-10) REVERT: A 329 GLU cc_start: 0.7231 (mp0) cc_final: 0.6874 (mp0) REVERT: A 375 TYR cc_start: 0.8610 (m-80) cc_final: 0.8333 (m-80) REVERT: A 396 ASP cc_start: 0.7636 (m-30) cc_final: 0.7348 (m-30) REVERT: B 22 ARG cc_start: 0.7502 (mtt90) cc_final: 0.6935 (mmm-85) REVERT: B 175 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7983 (mm-40) REVERT: B 212 ASP cc_start: 0.8118 (p0) cc_final: 0.7752 (p0) REVERT: B 258 ASP cc_start: 0.7447 (t70) cc_final: 0.6681 (t70) REVERT: S 18 ARG cc_start: 0.8083 (ttm170) cc_final: 0.7756 (ttt180) REVERT: S 167 GLN cc_start: 0.8604 (tt0) cc_final: 0.8313 (tt0) REVERT: S 201 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.8159 (m) outliers start: 28 outliers final: 24 residues processed: 228 average time/residue: 1.2983 time to fit residues: 313.7759 Evaluate side-chains 239 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 213 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 R residue 280 MET Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 291 ILE 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 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 198 THR 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 4 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS 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 = 0.3715 r_free = 0.3715 target = 0.132421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.115055 restraints weight = 11986.239| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.78 r_work: 0.3358 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9179 Z= 0.130 Angle : 0.560 11.425 12438 Z= 0.294 Chirality : 0.042 0.133 1408 Planarity : 0.004 0.042 1573 Dihedral : 4.490 38.964 1252 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.96 % Allowed : 17.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.26), residues: 1124 helix: 2.10 (0.27), residues: 379 sheet: 0.94 (0.30), residues: 302 loop : -0.46 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS B 62 PHE 0.016 0.001 PHE R 304 TYR 0.013 0.001 TYR S 178 ARG 0.004 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.04002 ( 453) hydrogen bonds : angle 4.87205 ( 1272) SS BOND : bond 0.00353 ( 2) SS BOND : angle 1.61660 ( 4) covalent geometry : bond 0.00299 ( 9176) covalent geometry : angle 0.55942 (12434) Misc. bond : bond 0.00044 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8613.15 seconds wall clock time: 148 minutes 52.95 seconds (8932.95 seconds total)