Starting phenix.real_space_refine on Wed Sep 17 12:24:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xoh_38529/09_2025/8xoh_38529.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xoh_38529/09_2025/8xoh_38529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xoh_38529/09_2025/8xoh_38529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xoh_38529/09_2025/8xoh_38529.map" model { file = "/net/cci-nas-00/data/ceres_data/8xoh_38529/09_2025/8xoh_38529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xoh_38529/09_2025/8xoh_38529.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 5600 2.51 5 N 1529 2.21 5 O 1625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8809 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1875 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Chain: "B" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2581 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1746 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2171 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 7, 'TRANS': 257} Chain breaks: 3 Time building chain proxies: 1.95, per 1000 atoms: 0.22 Number of scatterers: 8809 At special positions: 0 Unit cell: (111.384, 118.881, 108.171, 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 55 16.00 O 1625 8.00 N 1529 7.00 C 5600 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 358.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2098 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 41.7% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 15 through 40 removed outlier: 3.792A pdb=" N ALA A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.515A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.601A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 4.035A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 4.335A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.986A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 220 through 224 removed outlier: 4.008A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 25 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'R' and resid 52 through 87 removed outlier: 3.749A pdb=" N GLY R 58 " --> pdb=" O GLN R 54 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE R 70 " --> pdb=" O THR R 66 " (cutoff:3.500A) Proline residue: R 71 - end of helix removed outlier: 3.555A pdb=" N PHE R 87 " --> pdb=" O VAL R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 91 removed outlier: 3.524A pdb=" N MET R 91 " --> pdb=" O ARG R 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 88 through 91' Processing helix chain 'R' and resid 92 through 116 removed outlier: 3.705A pdb=" N LEU R 96 " --> pdb=" O THR R 92 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR R 97 " --> pdb=" O ILE R 93 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU R 113 " --> pdb=" O VAL R 109 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE R 114 " --> pdb=" O ALA R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 124 removed outlier: 3.590A pdb=" N TYR R 123 " --> pdb=" O LEU R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 160 Processing helix chain 'R' and resid 163 through 168 removed outlier: 3.615A pdb=" N SER R 166 " --> pdb=" O MET R 163 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU R 167 " --> pdb=" O ARG R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 200 Proline residue: R 192 - end of helix Processing helix chain 'R' and resid 211 through 223 Processing helix chain 'R' and resid 223 through 248 Processing helix chain 'R' and resid 254 through 285 removed outlier: 3.545A pdb=" N LEU R 258 " --> pdb=" O ARG R 254 " (cutoff:3.500A) Proline residue: R 274 - end of helix Processing helix chain 'R' and resid 302 through 325 removed outlier: 3.931A pdb=" N SER R 317 " --> pdb=" O ALA R 313 " (cutoff:3.500A) Proline residue: R 321 - end of helix Processing helix chain 'R' and resid 328 through 342 removed outlier: 3.578A pdb=" N ARG R 332 " --> pdb=" O GLY R 328 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.891A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.660A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.502A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.790A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.599A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.714A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.477A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.751A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.784A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.463A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.012A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1326 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: 1.43 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2012 1.33 - 1.45: 1970 1.45 - 1.57: 4927 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 8989 Sorted by residual: bond pdb=" C THR A 325 " pdb=" N PRO A 326 " ideal model delta sigma weight residual 1.329 1.365 -0.036 1.25e-02 6.40e+03 8.13e+00 bond pdb=" C LEU R 304 " pdb=" O LEU R 304 " ideal model delta sigma weight residual 1.236 1.210 0.026 1.15e-02 7.56e+03 5.22e+00 bond pdb=" CB ASP A 272 " pdb=" CG ASP A 272 " ideal model delta sigma weight residual 1.516 1.465 0.051 2.50e-02 1.60e+03 4.16e+00 bond pdb=" C ASP R 111 " pdb=" O ASP R 111 " ideal model delta sigma weight residual 1.236 1.210 0.026 1.29e-02 6.01e+03 4.04e+00 bond pdb=" N THR G 6 " pdb=" CA THR G 6 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 ... (remaining 8984 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 12036 2.02 - 4.05: 126 4.05 - 6.07: 5 6.07 - 8.10: 1 8.10 - 10.12: 1 Bond angle restraints: 12169 Sorted by residual: angle pdb=" C THR A 325 " pdb=" N PRO A 326 " pdb=" CA PRO A 326 " ideal model delta sigma weight residual 120.14 114.67 5.47 1.06e+00 8.90e-01 2.66e+01 angle pdb=" C SER R 325 " pdb=" N PHE R 326 " pdb=" CA PHE R 326 " ideal model delta sigma weight residual 122.65 116.64 6.01 1.60e+00 3.91e-01 1.41e+01 angle pdb=" CB LYS G 32 " pdb=" CG LYS G 32 " pdb=" CD LYS G 32 " ideal model delta sigma weight residual 111.30 118.75 -7.45 2.30e+00 1.89e-01 1.05e+01 angle pdb=" N VAL A 241 " pdb=" CA VAL A 241 " pdb=" C VAL A 241 " ideal model delta sigma weight residual 110.05 106.84 3.21 1.09e+00 8.42e-01 8.69e+00 angle pdb=" CA PRO A 326 " pdb=" C PRO A 326 " pdb=" O PRO A 326 " ideal model delta sigma weight residual 121.86 118.38 3.48 1.22e+00 6.72e-01 8.13e+00 ... (remaining 12164 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4753 17.96 - 35.92: 459 35.92 - 53.88: 89 53.88 - 71.84: 22 71.84 - 89.81: 9 Dihedral angle restraints: 5332 sinusoidal: 2092 harmonic: 3240 Sorted by residual: dihedral pdb=" CA THR A 364 " pdb=" C THR A 364 " pdb=" N CYS A 365 " pdb=" CA CYS A 365 " ideal model delta harmonic sigma weight residual 180.00 159.86 20.14 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA PHE R 326 " pdb=" C PHE R 326 " pdb=" N LEU R 327 " pdb=" CA LEU R 327 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA ASP R 111 " pdb=" CB ASP R 111 " pdb=" CG ASP R 111 " pdb=" OD1 ASP R 111 " ideal model delta sinusoidal sigma weight residual -30.00 -90.52 60.52 1 2.00e+01 2.50e-03 1.22e+01 ... (remaining 5329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1103 0.044 - 0.088: 182 0.088 - 0.132: 88 0.132 - 0.176: 4 0.176 - 0.220: 1 Chirality restraints: 1378 Sorted by residual: chirality pdb=" CA ASP E 73 " pdb=" N ASP E 73 " pdb=" C ASP E 73 " pdb=" CB ASP E 73 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ASN R 100 " pdb=" N ASN R 100 " pdb=" C ASN R 100 " pdb=" CB ASN R 100 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.40e-01 chirality pdb=" CA ASP R 111 " pdb=" N ASP R 111 " pdb=" C ASP R 111 " pdb=" CB ASP R 111 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 1375 not shown) Planarity restraints: 1546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 180 " 0.037 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO E 181 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO E 181 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 181 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 13 " 0.171 9.50e-02 1.11e+02 7.67e-02 3.88e+00 pdb=" NE ARG G 13 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG G 13 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG G 13 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG G 13 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 325 " 0.007 2.00e-02 2.50e+03 1.28e-02 1.65e+00 pdb=" C SER R 325 " -0.022 2.00e-02 2.50e+03 pdb=" O SER R 325 " 0.008 2.00e-02 2.50e+03 pdb=" N PHE R 326 " 0.008 2.00e-02 2.50e+03 ... (remaining 1543 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1237 2.75 - 3.29: 8899 3.29 - 3.83: 14753 3.83 - 4.36: 18021 4.36 - 4.90: 31192 Nonbonded interactions: 74102 Sorted by model distance: nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.215 3.040 nonbonded pdb=" O ASP B 195 " pdb=" OG1 THR B 196 " model vdw 2.237 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.267 3.040 nonbonded pdb=" OD1 ASP A 249 " pdb=" OG SER A 251 " model vdw 2.287 3.040 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.293 3.040 ... (remaining 74097 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: 0.700 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.110 Find NCS groups from input model: 0.050 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 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 : 0.003 0.051 8989 Z= 0.156 Angle : 0.557 10.123 12169 Z= 0.325 Chirality : 0.041 0.220 1378 Planarity : 0.004 0.077 1546 Dihedral : 15.157 89.805 3234 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.21 % Allowed : 13.66 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.26), residues: 1092 helix: 1.45 (0.25), residues: 408 sheet: -0.34 (0.31), residues: 258 loop : 0.28 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 13 TYR 0.019 0.001 TYR A 311 PHE 0.016 0.001 PHE E 68 TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS R 197 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8989) covalent geometry : angle 0.55742 (12169) hydrogen bonds : bond 0.15771 ( 468) hydrogen bonds : angle 6.78337 ( 1326) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 211 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 391 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.8033 (m-80) REVERT: B 101 MET cc_start: 0.8881 (mtp) cc_final: 0.8641 (mtp) REVERT: E 34 MET cc_start: 0.8982 (mmt) cc_final: 0.8772 (mmt) REVERT: E 142 GLN cc_start: 0.6582 (mt0) cc_final: 0.6316 (mt0) REVERT: E 229 CYS cc_start: 0.8419 (p) cc_final: 0.8110 (p) REVERT: R 135 LEU cc_start: 0.8393 (mt) cc_final: 0.8019 (mp) outliers start: 2 outliers final: 1 residues processed: 212 average time/residue: 0.1194 time to fit residues: 33.3267 Evaluate side-chains 176 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 174 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain R residue 304 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN E 77 ASN E 194 ASN E 232 HIS R 282 HIS R 310 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.160357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.122921 restraints weight = 10918.243| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.50 r_work: 0.3164 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 8989 Z= 0.250 Angle : 0.639 7.905 12169 Z= 0.344 Chirality : 0.046 0.205 1378 Planarity : 0.004 0.036 1546 Dihedral : 5.662 59.369 1217 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.92 % Allowed : 16.06 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.25), residues: 1092 helix: 1.47 (0.25), residues: 400 sheet: -0.64 (0.31), residues: 241 loop : 0.05 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 13 TYR 0.015 0.002 TYR R 324 PHE 0.018 0.002 PHE E 68 TRP 0.017 0.002 TRP B 339 HIS 0.005 0.001 HIS E 232 Details of bonding type rmsd covalent geometry : bond 0.00572 ( 8989) covalent geometry : angle 0.63913 (12169) hydrogen bonds : bond 0.04950 ( 468) hydrogen bonds : angle 5.34675 ( 1326) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 356 ARG cc_start: 0.7827 (mtp85) cc_final: 0.7619 (mtp85) REVERT: A 390 GLU cc_start: 0.8718 (tt0) cc_final: 0.8491 (tt0) REVERT: A 391 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.8069 (m-80) REVERT: B 215 GLU cc_start: 0.8686 (tp30) cc_final: 0.8460 (tp30) REVERT: B 254 ASP cc_start: 0.8426 (t70) cc_final: 0.8074 (t0) REVERT: E 68 PHE cc_start: 0.6313 (m-80) cc_final: 0.5266 (m-10) REVERT: E 80 PHE cc_start: 0.7894 (m-80) cc_final: 0.7252 (m-80) REVERT: E 83 MET cc_start: 0.8135 (mmt) cc_final: 0.7327 (mmt) REVERT: E 90 ASP cc_start: 0.7884 (m-30) cc_final: 0.7428 (m-30) REVERT: E 142 GLN cc_start: 0.6580 (mt0) cc_final: 0.5975 (mt0) REVERT: E 229 CYS cc_start: 0.8627 (p) cc_final: 0.8317 (p) REVERT: G 21 MET cc_start: 0.7647 (mtp) cc_final: 0.6853 (tpp) REVERT: G 48 ASP cc_start: 0.8511 (t0) cc_final: 0.8168 (t0) REVERT: R 91 MET cc_start: 0.6566 (mtm) cc_final: 0.5898 (mtt) REVERT: R 135 LEU cc_start: 0.8504 (mt) cc_final: 0.8124 (mp) REVERT: R 154 ASP cc_start: 0.8871 (t0) cc_final: 0.8046 (t0) outliers start: 28 outliers final: 18 residues processed: 207 average time/residue: 0.0945 time to fit residues: 27.1152 Evaluate side-chains 186 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 141 MET Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 197 HIS Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain R residue 323 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 75 optimal weight: 9.9990 chunk 14 optimal weight: 0.0770 chunk 81 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.163558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.126384 restraints weight = 10733.939| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.46 r_work: 0.3219 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8989 Z= 0.134 Angle : 0.537 7.289 12169 Z= 0.290 Chirality : 0.042 0.271 1378 Planarity : 0.003 0.030 1546 Dihedral : 5.001 59.976 1215 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.82 % Allowed : 16.16 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.25), residues: 1092 helix: 1.65 (0.25), residues: 401 sheet: -0.67 (0.30), residues: 242 loop : -0.02 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 13 TYR 0.011 0.001 TYR A 311 PHE 0.012 0.001 PHE E 68 TRP 0.019 0.002 TRP B 82 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8989) covalent geometry : angle 0.53662 (12169) hydrogen bonds : bond 0.04254 ( 468) hydrogen bonds : angle 4.97774 ( 1326) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7537 (t0) cc_final: 0.7199 (t0) REVERT: A 29 GLN cc_start: 0.8816 (tp-100) cc_final: 0.8409 (tp-100) REVERT: A 299 GLU cc_start: 0.8550 (pt0) cc_final: 0.8298 (pt0) REVERT: A 356 ARG cc_start: 0.7770 (mtp85) cc_final: 0.7533 (mtp85) REVERT: A 391 TYR cc_start: 0.8700 (OUTLIER) cc_final: 0.8025 (m-80) REVERT: B 249 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8083 (t) REVERT: B 254 ASP cc_start: 0.8379 (t70) cc_final: 0.7994 (t0) REVERT: E 68 PHE cc_start: 0.6167 (m-80) cc_final: 0.5163 (m-10) REVERT: E 80 PHE cc_start: 0.7918 (m-80) cc_final: 0.7601 (m-80) REVERT: E 82 GLN cc_start: 0.8093 (tp40) cc_final: 0.7701 (tp40) REVERT: E 83 MET cc_start: 0.8140 (mmt) cc_final: 0.7308 (mmt) REVERT: E 90 ASP cc_start: 0.7693 (m-30) cc_final: 0.7268 (m-30) REVERT: E 142 GLN cc_start: 0.6365 (mt0) cc_final: 0.6161 (mt0) REVERT: G 32 LYS cc_start: 0.7814 (tptm) cc_final: 0.7533 (tppt) REVERT: R 91 MET cc_start: 0.6498 (mtm) cc_final: 0.5897 (mtt) REVERT: R 154 ASP cc_start: 0.8715 (t0) cc_final: 0.7422 (t0) outliers start: 27 outliers final: 14 residues processed: 207 average time/residue: 0.1072 time to fit residues: 30.1081 Evaluate side-chains 185 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 149 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 82 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN E 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.162668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.125548 restraints weight = 10924.360| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.46 r_work: 0.3129 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8989 Z= 0.159 Angle : 0.542 6.661 12169 Z= 0.290 Chirality : 0.043 0.214 1378 Planarity : 0.003 0.031 1546 Dihedral : 4.925 59.858 1215 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.23 % Allowed : 17.00 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.25), residues: 1092 helix: 1.71 (0.25), residues: 407 sheet: -0.66 (0.30), residues: 246 loop : -0.12 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 13 TYR 0.011 0.001 TYR R 338 PHE 0.013 0.001 PHE R 326 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 8989) covalent geometry : angle 0.54236 (12169) hydrogen bonds : bond 0.04099 ( 468) hydrogen bonds : angle 4.84289 ( 1326) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7497 (t0) cc_final: 0.7204 (t0) REVERT: A 29 GLN cc_start: 0.8770 (tp-100) cc_final: 0.8360 (tp-100) REVERT: A 220 HIS cc_start: 0.8576 (m170) cc_final: 0.8124 (m-70) REVERT: A 299 GLU cc_start: 0.8363 (pt0) cc_final: 0.8112 (pt0) REVERT: A 356 ARG cc_start: 0.7762 (mtp85) cc_final: 0.7499 (mtp85) REVERT: A 391 TYR cc_start: 0.8697 (OUTLIER) cc_final: 0.7941 (m-80) REVERT: B 254 ASP cc_start: 0.8324 (t70) cc_final: 0.7906 (t0) REVERT: E 68 PHE cc_start: 0.6207 (m-80) cc_final: 0.4906 (m-10) REVERT: E 80 PHE cc_start: 0.7851 (m-80) cc_final: 0.7538 (m-80) REVERT: E 82 GLN cc_start: 0.8053 (tp40) cc_final: 0.7562 (tp40) REVERT: E 83 MET cc_start: 0.8196 (mmt) cc_final: 0.7019 (mmt) REVERT: E 90 ASP cc_start: 0.7601 (m-30) cc_final: 0.7156 (m-30) REVERT: G 32 LYS cc_start: 0.7759 (tptm) cc_final: 0.7458 (tppt) REVERT: R 82 VAL cc_start: 0.8144 (m) cc_final: 0.7861 (p) REVERT: R 141 MET cc_start: 0.7812 (mtp) cc_final: 0.7510 (mtt) REVERT: R 154 ASP cc_start: 0.8798 (t70) cc_final: 0.7445 (t0) outliers start: 31 outliers final: 26 residues processed: 198 average time/residue: 0.1132 time to fit residues: 30.0397 Evaluate side-chains 193 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain R residue 240 VAL Chi-restraints excluded: chain R residue 282 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 73 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.160010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.122838 restraints weight = 10932.429| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.51 r_work: 0.3070 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8989 Z= 0.236 Angle : 0.591 7.102 12169 Z= 0.316 Chirality : 0.045 0.193 1378 Planarity : 0.004 0.029 1546 Dihedral : 5.083 59.750 1215 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.69 % Allowed : 16.79 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.25), residues: 1092 helix: 1.77 (0.25), residues: 403 sheet: -0.71 (0.30), residues: 253 loop : -0.24 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 27 TYR 0.015 0.002 TYR R 65 PHE 0.016 0.002 PHE R 326 TRP 0.014 0.002 TRP B 82 HIS 0.005 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00543 ( 8989) covalent geometry : angle 0.59095 (12169) hydrogen bonds : bond 0.04340 ( 468) hydrogen bonds : angle 4.94268 ( 1326) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7515 (t0) cc_final: 0.7241 (t0) REVERT: A 29 GLN cc_start: 0.8712 (tp-100) cc_final: 0.8309 (tp-100) REVERT: A 220 HIS cc_start: 0.8450 (m170) cc_final: 0.8036 (m-70) REVERT: A 299 GLU cc_start: 0.8283 (pt0) cc_final: 0.8051 (pt0) REVERT: A 391 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.7870 (m-80) REVERT: B 234 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.7406 (m-80) REVERT: B 254 ASP cc_start: 0.8350 (t70) cc_final: 0.7897 (t0) REVERT: E 68 PHE cc_start: 0.6314 (m-80) cc_final: 0.5143 (m-10) REVERT: E 80 PHE cc_start: 0.7888 (m-80) cc_final: 0.7310 (m-80) REVERT: E 82 GLN cc_start: 0.7973 (tp40) cc_final: 0.7444 (tp40) REVERT: E 83 MET cc_start: 0.8209 (mmt) cc_final: 0.7025 (mmt) REVERT: E 90 ASP cc_start: 0.7882 (m-30) cc_final: 0.7403 (m-30) REVERT: G 32 LYS cc_start: 0.7785 (tptm) cc_final: 0.7472 (tppt) REVERT: R 57 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7257 (pt) REVERT: R 82 VAL cc_start: 0.8187 (m) cc_final: 0.7893 (p) REVERT: R 120 HIS cc_start: 0.6125 (OUTLIER) cc_final: 0.5829 (m90) REVERT: R 151 MET cc_start: 0.8313 (mtp) cc_final: 0.8019 (ttm) REVERT: R 154 ASP cc_start: 0.8867 (t70) cc_final: 0.7513 (t0) outliers start: 45 outliers final: 35 residues processed: 208 average time/residue: 0.1078 time to fit residues: 30.3410 Evaluate side-chains 205 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 120 HIS Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 197 HIS Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain R residue 240 VAL Chi-restraints excluded: chain R residue 282 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 9 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN E 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.163348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.126081 restraints weight = 10796.691| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.46 r_work: 0.3218 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8989 Z= 0.127 Angle : 0.520 7.326 12169 Z= 0.279 Chirality : 0.042 0.182 1378 Planarity : 0.003 0.030 1546 Dihedral : 4.821 59.986 1215 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.38 % Allowed : 17.52 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.25), residues: 1092 helix: 1.86 (0.25), residues: 407 sheet: -0.64 (0.30), residues: 247 loop : -0.25 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 27 TYR 0.013 0.001 TYR R 65 PHE 0.012 0.001 PHE R 326 TRP 0.020 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 8989) covalent geometry : angle 0.52030 (12169) hydrogen bonds : bond 0.03876 ( 468) hydrogen bonds : angle 4.71755 ( 1326) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 179 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7491 (t0) cc_final: 0.7197 (t0) REVERT: A 29 GLN cc_start: 0.8757 (tp-100) cc_final: 0.8377 (tp-100) REVERT: A 220 HIS cc_start: 0.8467 (m170) cc_final: 0.8260 (m90) REVERT: A 299 GLU cc_start: 0.8300 (pt0) cc_final: 0.8074 (pt0) REVERT: A 391 TYR cc_start: 0.8725 (OUTLIER) cc_final: 0.7966 (m-80) REVERT: B 215 GLU cc_start: 0.8617 (tp30) cc_final: 0.8158 (tp30) REVERT: B 234 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.7422 (m-80) REVERT: B 254 ASP cc_start: 0.8321 (t70) cc_final: 0.7949 (t0) REVERT: E 18 ARG cc_start: 0.6370 (tpp-160) cc_final: 0.5833 (tpp80) REVERT: E 34 MET cc_start: 0.9120 (mmt) cc_final: 0.8878 (mmm) REVERT: E 68 PHE cc_start: 0.6197 (m-80) cc_final: 0.5045 (m-10) REVERT: E 72 ARG cc_start: 0.8402 (ttm-80) cc_final: 0.7937 (ttm-80) REVERT: E 80 PHE cc_start: 0.7944 (m-80) cc_final: 0.7578 (m-80) REVERT: E 82 GLN cc_start: 0.8053 (tp40) cc_final: 0.7571 (tp40) REVERT: E 83 MET cc_start: 0.8174 (mmt) cc_final: 0.7161 (mmt) REVERT: E 90 ASP cc_start: 0.7743 (m-30) cc_final: 0.7333 (m-30) REVERT: E 166 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8902 (tt) REVERT: E 212 PHE cc_start: 0.8401 (m-80) cc_final: 0.8148 (m-10) REVERT: G 32 LYS cc_start: 0.7798 (tptm) cc_final: 0.7526 (tppt) REVERT: R 57 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7377 (pt) REVERT: R 154 ASP cc_start: 0.8861 (t70) cc_final: 0.7496 (t0) outliers start: 42 outliers final: 26 residues processed: 205 average time/residue: 0.1051 time to fit residues: 29.4808 Evaluate side-chains 201 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain R residue 282 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 68 optimal weight: 0.0980 chunk 3 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN R 120 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.161750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.124590 restraints weight = 10903.992| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.47 r_work: 0.3126 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8989 Z= 0.175 Angle : 0.543 7.037 12169 Z= 0.291 Chirality : 0.042 0.159 1378 Planarity : 0.003 0.029 1546 Dihedral : 4.851 59.594 1215 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.07 % Allowed : 18.35 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.25), residues: 1092 helix: 1.94 (0.25), residues: 407 sheet: -0.62 (0.30), residues: 247 loop : -0.29 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 27 TYR 0.010 0.001 TYR R 338 PHE 0.014 0.002 PHE R 326 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 8989) covalent geometry : angle 0.54283 (12169) hydrogen bonds : bond 0.03966 ( 468) hydrogen bonds : angle 4.73347 ( 1326) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 170 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7501 (t0) cc_final: 0.7225 (t0) REVERT: A 29 GLN cc_start: 0.8706 (tp-100) cc_final: 0.8281 (tp-100) REVERT: A 220 HIS cc_start: 0.8465 (m170) cc_final: 0.8256 (m90) REVERT: A 391 TYR cc_start: 0.8709 (OUTLIER) cc_final: 0.7870 (m-80) REVERT: B 215 GLU cc_start: 0.8706 (tp30) cc_final: 0.8246 (tp30) REVERT: B 234 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.7551 (m-80) REVERT: B 254 ASP cc_start: 0.8316 (t70) cc_final: 0.7905 (t0) REVERT: E 34 MET cc_start: 0.9178 (mmt) cc_final: 0.8913 (mmm) REVERT: E 68 PHE cc_start: 0.6229 (m-80) cc_final: 0.5105 (m-10) REVERT: E 72 ARG cc_start: 0.8377 (ttm-80) cc_final: 0.8126 (ttm-80) REVERT: E 80 PHE cc_start: 0.7920 (m-80) cc_final: 0.7535 (m-80) REVERT: E 82 GLN cc_start: 0.8016 (tp40) cc_final: 0.7534 (tp40) REVERT: E 83 MET cc_start: 0.8162 (mmt) cc_final: 0.7149 (mmt) REVERT: E 90 ASP cc_start: 0.7719 (m-30) cc_final: 0.7274 (m-30) REVERT: E 166 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8908 (tt) REVERT: E 212 PHE cc_start: 0.8369 (m-80) cc_final: 0.8116 (m-10) REVERT: G 32 LYS cc_start: 0.7786 (tptm) cc_final: 0.7465 (tppt) REVERT: R 57 ILE cc_start: 0.7682 (OUTLIER) cc_final: 0.7394 (pt) REVERT: R 154 ASP cc_start: 0.8863 (t70) cc_final: 0.7492 (t0) REVERT: R 342 LYS cc_start: 0.5041 (mmtm) cc_final: 0.4206 (mmtt) outliers start: 39 outliers final: 31 residues processed: 195 average time/residue: 0.0946 time to fit residues: 25.3684 Evaluate side-chains 202 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain R residue 282 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 81 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.164755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.127655 restraints weight = 10785.563| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.46 r_work: 0.3182 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8989 Z= 0.115 Angle : 0.503 7.006 12169 Z= 0.269 Chirality : 0.041 0.151 1378 Planarity : 0.003 0.030 1546 Dihedral : 4.616 59.222 1215 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.55 % Allowed : 19.40 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.25), residues: 1092 helix: 2.13 (0.25), residues: 401 sheet: -0.63 (0.28), residues: 272 loop : -0.12 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 27 TYR 0.015 0.001 TYR R 65 PHE 0.011 0.001 PHE R 326 TRP 0.020 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8989) covalent geometry : angle 0.50325 (12169) hydrogen bonds : bond 0.03672 ( 468) hydrogen bonds : angle 4.53253 ( 1326) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7477 (t0) cc_final: 0.7197 (t0) REVERT: A 29 GLN cc_start: 0.8714 (tp-100) cc_final: 0.8303 (tp-100) REVERT: A 220 HIS cc_start: 0.8397 (m170) cc_final: 0.8167 (m90) REVERT: A 391 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.7891 (m-80) REVERT: B 59 TYR cc_start: 0.8952 (OUTLIER) cc_final: 0.8393 (m-80) REVERT: B 215 GLU cc_start: 0.8580 (tp30) cc_final: 0.8172 (tp30) REVERT: B 234 PHE cc_start: 0.9090 (OUTLIER) cc_final: 0.7388 (m-80) REVERT: B 254 ASP cc_start: 0.8278 (t70) cc_final: 0.7872 (t0) REVERT: E 34 MET cc_start: 0.9137 (mmt) cc_final: 0.8927 (mmm) REVERT: E 68 PHE cc_start: 0.6060 (m-80) cc_final: 0.4947 (m-10) REVERT: E 72 ARG cc_start: 0.8335 (ttm-80) cc_final: 0.8125 (ttm-80) REVERT: E 82 GLN cc_start: 0.8025 (tp40) cc_final: 0.7531 (tp40) REVERT: E 83 MET cc_start: 0.8121 (mmt) cc_final: 0.7090 (mmt) REVERT: E 90 ASP cc_start: 0.7479 (m-30) cc_final: 0.7189 (m-30) REVERT: E 166 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8904 (tt) REVERT: G 32 LYS cc_start: 0.7431 (tptm) cc_final: 0.7082 (tppt) REVERT: R 57 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.7454 (pt) REVERT: R 64 LEU cc_start: 0.8564 (tp) cc_final: 0.8315 (pp) REVERT: R 154 ASP cc_start: 0.8795 (t70) cc_final: 0.7366 (t0) REVERT: R 342 LYS cc_start: 0.5051 (mmtm) cc_final: 0.4199 (mmtt) outliers start: 34 outliers final: 22 residues processed: 205 average time/residue: 0.0963 time to fit residues: 27.3474 Evaluate side-chains 199 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 152 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 106 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 88 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN E 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.164074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.127020 restraints weight = 10737.211| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.43 r_work: 0.3149 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8989 Z= 0.135 Angle : 0.533 8.241 12169 Z= 0.280 Chirality : 0.041 0.174 1378 Planarity : 0.003 0.029 1546 Dihedral : 4.605 58.623 1215 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.07 % Allowed : 20.23 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.25), residues: 1092 helix: 2.11 (0.25), residues: 399 sheet: -0.67 (0.29), residues: 258 loop : -0.11 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 27 TYR 0.015 0.001 TYR R 65 PHE 0.014 0.001 PHE E 212 TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8989) covalent geometry : angle 0.53297 (12169) hydrogen bonds : bond 0.03735 ( 468) hydrogen bonds : angle 4.52094 ( 1326) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7456 (t0) cc_final: 0.7196 (t0) REVERT: A 29 GLN cc_start: 0.8712 (tp-100) cc_final: 0.8297 (tp-100) REVERT: A 220 HIS cc_start: 0.8409 (m170) cc_final: 0.8183 (m90) REVERT: A 368 ASP cc_start: 0.7519 (t0) cc_final: 0.6860 (p0) REVERT: A 391 TYR cc_start: 0.8682 (OUTLIER) cc_final: 0.7890 (m-80) REVERT: B 215 GLU cc_start: 0.8599 (tp30) cc_final: 0.8208 (tp30) REVERT: B 234 PHE cc_start: 0.9153 (OUTLIER) cc_final: 0.7371 (m-80) REVERT: B 254 ASP cc_start: 0.8272 (t70) cc_final: 0.7857 (t0) REVERT: E 34 MET cc_start: 0.9120 (mmt) cc_final: 0.8917 (mmm) REVERT: E 68 PHE cc_start: 0.6035 (m-80) cc_final: 0.4913 (m-10) REVERT: E 72 ARG cc_start: 0.8259 (ttm-80) cc_final: 0.8038 (ttm-80) REVERT: E 82 GLN cc_start: 0.7970 (tp40) cc_final: 0.7442 (tp40) REVERT: E 83 MET cc_start: 0.8181 (mmt) cc_final: 0.7038 (mmt) REVERT: E 90 ASP cc_start: 0.7485 (m-30) cc_final: 0.7156 (m-30) REVERT: E 166 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8890 (tt) REVERT: G 32 LYS cc_start: 0.7403 (tptm) cc_final: 0.7192 (tppt) REVERT: R 57 ILE cc_start: 0.7797 (OUTLIER) cc_final: 0.7538 (pt) REVERT: R 64 LEU cc_start: 0.8488 (tp) cc_final: 0.8241 (pp) REVERT: R 154 ASP cc_start: 0.8799 (t70) cc_final: 0.7281 (t0) outliers start: 39 outliers final: 27 residues processed: 203 average time/residue: 0.1020 time to fit residues: 28.5907 Evaluate side-chains 200 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 240 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 58 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.164604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.127466 restraints weight = 10787.035| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.48 r_work: 0.3150 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8989 Z= 0.124 Angle : 0.524 7.871 12169 Z= 0.277 Chirality : 0.041 0.157 1378 Planarity : 0.003 0.030 1546 Dihedral : 4.556 58.228 1215 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.44 % Allowed : 20.54 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.25), residues: 1092 helix: 2.23 (0.25), residues: 393 sheet: -0.65 (0.29), residues: 253 loop : -0.15 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 27 TYR 0.015 0.001 TYR R 65 PHE 0.012 0.001 PHE R 326 TRP 0.018 0.001 TRP B 82 HIS 0.006 0.001 HIS R 302 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8989) covalent geometry : angle 0.52367 (12169) hydrogen bonds : bond 0.03669 ( 468) hydrogen bonds : angle 4.47406 ( 1326) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 177 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7492 (t0) cc_final: 0.7224 (t0) REVERT: A 29 GLN cc_start: 0.8711 (tp-100) cc_final: 0.8298 (tp-100) REVERT: A 220 HIS cc_start: 0.8400 (m170) cc_final: 0.8176 (m90) REVERT: A 368 ASP cc_start: 0.7556 (t0) cc_final: 0.6894 (p0) REVERT: A 391 TYR cc_start: 0.8645 (OUTLIER) cc_final: 0.8205 (m-80) REVERT: B 215 GLU cc_start: 0.8530 (tp30) cc_final: 0.8211 (tp30) REVERT: B 234 PHE cc_start: 0.9151 (OUTLIER) cc_final: 0.7351 (m-80) REVERT: B 254 ASP cc_start: 0.8273 (t70) cc_final: 0.7848 (t0) REVERT: E 72 ARG cc_start: 0.8232 (ttm-80) cc_final: 0.8008 (ttm-80) REVERT: E 82 GLN cc_start: 0.7925 (tp40) cc_final: 0.7394 (tp40) REVERT: E 83 MET cc_start: 0.8116 (mmt) cc_final: 0.7519 (mmt) REVERT: E 166 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8883 (tt) REVERT: G 32 LYS cc_start: 0.7439 (tptm) cc_final: 0.7204 (tppt) REVERT: R 57 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7513 (pt) REVERT: R 154 ASP cc_start: 0.8790 (t70) cc_final: 0.8584 (t70) REVERT: R 326 PHE cc_start: 0.7125 (p90) cc_final: 0.6903 (p90) REVERT: R 342 LYS cc_start: 0.4938 (mmtm) cc_final: 0.4148 (mmtt) outliers start: 33 outliers final: 27 residues processed: 199 average time/residue: 0.1041 time to fit residues: 28.4414 Evaluate side-chains 200 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 240 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 59 optimal weight: 0.0040 chunk 101 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 28 optimal weight: 0.3980 chunk 92 optimal weight: 0.9980 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.165568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.128774 restraints weight = 10646.963| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.42 r_work: 0.3164 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8989 Z= 0.116 Angle : 0.530 8.010 12169 Z= 0.278 Chirality : 0.041 0.154 1378 Planarity : 0.003 0.030 1546 Dihedral : 4.491 57.870 1215 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.44 % Allowed : 20.75 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.25), residues: 1092 helix: 2.30 (0.25), residues: 393 sheet: -0.65 (0.29), residues: 265 loop : -0.21 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 27 TYR 0.014 0.001 TYR R 65 PHE 0.012 0.001 PHE R 326 TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 8989) covalent geometry : angle 0.53004 (12169) hydrogen bonds : bond 0.03587 ( 468) hydrogen bonds : angle 4.42898 ( 1326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2998.40 seconds wall clock time: 51 minutes 59.24 seconds (3119.24 seconds total)