Starting phenix.real_space_refine on Wed Aug 5 13:21:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/26xh_80947/08_2026/26xh_80947.cif Found real_map, /net/cci-nas-00/data/ceres_data/26xh_80947/08_2026/26xh_80947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/26xh_80947/08_2026/26xh_80947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/26xh_80947/08_2026/26xh_80947.map" model { file = "/net/cci-nas-00/data/ceres_data/26xh_80947/08_2026/26xh_80947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/26xh_80947/08_2026/26xh_80947.cif" } resolution = 2.82 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= 0.079 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 66 5.16 5 C 6290 2.51 5 N 1704 2.21 5 O 1855 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9915 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1864 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 432 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 964 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2344 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 10, 'TRANS': 281} Chain: "B" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2566 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "S" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1737 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "R" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'MAE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.28, per 1000 atoms: 0.23 Number of scatterers: 9915 At special positions: 0 Unit cell: (89.38, 126.28, 129.56, 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 66 16.00 O 1855 8.00 N 1704 7.00 C 6290 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 183 " distance=2.23 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: 1.12 Conformation dependent library (CDL) restraints added in 417.3 milliseconds 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2382 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 15 sheets defined 36.6% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 15 through 39 Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.519A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.500A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.591A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.689A pdb=" N ARG A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.794A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) 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 'N' and resid 28 through 32 removed outlier: 3.807A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 28 through 34 Processing helix chain 'R' and resid 34 through 60 removed outlier: 4.114A pdb=" N VAL R 38 " --> pdb=" O HIS R 34 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR R 40 " --> pdb=" O LEU R 36 " (cutoff:3.500A) Proline residue: R 49 - end of helix Processing helix chain 'R' and resid 66 through 95 Proline residue: R 87 - end of helix Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 141 through 145 Processing helix chain 'R' and resid 146 through 166 removed outlier: 3.860A pdb=" N ALA R 150 " --> pdb=" O LYS R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 171 removed outlier: 3.513A pdb=" N PHE R 170 " --> pdb=" O PRO R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 207 removed outlier: 3.949A pdb=" N TRP R 197 " --> pdb=" O ASN R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 227 Processing helix chain 'R' and resid 233 through 270 Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 273 through 293 Proline residue: R 289 - end of helix Processing helix chain 'R' and resid 293 through 303 removed outlier: 3.707A pdb=" N VAL R 303 " --> pdb=" O LEU R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 317 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 220 through 224 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.647A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.953A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'R' and resid 174 through 176 Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.517A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.649A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.753A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.864A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.862A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.470A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.785A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.813A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB6, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.742A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1404 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: 1.72 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3202 1.34 - 1.46: 1856 1.46 - 1.58: 4968 1.58 - 1.70: 0 1.70 - 1.82: 91 Bond restraints: 10117 Sorted by residual: bond pdb=" CA ASN G 24 " pdb=" CB ASN G 24 " ideal model delta sigma weight residual 1.524 1.555 -0.031 1.30e-02 5.92e+03 5.85e+00 bond pdb=" C1 MAE R 401 " pdb=" C2 MAE R 401 " ideal model delta sigma weight residual 1.513 1.476 0.037 2.00e-02 2.50e+03 3.37e+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 3.05e+00 bond pdb=" N SER B 281 " pdb=" CA SER B 281 " ideal model delta sigma weight residual 1.456 1.479 -0.022 1.31e-02 5.83e+03 2.90e+00 bond pdb=" N GLU B 3 " pdb=" CA GLU B 3 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.70e+00 ... (remaining 10112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 13485 1.77 - 3.54: 188 3.54 - 5.31: 35 5.31 - 7.08: 5 7.08 - 8.85: 3 Bond angle restraints: 13716 Sorted by residual: angle pdb=" N GLN N 3 " pdb=" CA GLN N 3 " pdb=" C GLN N 3 " ideal model delta sigma weight residual 108.76 115.91 -7.15 1.69e+00 3.50e-01 1.79e+01 angle pdb=" N VAL N 64 " pdb=" CA VAL N 64 " pdb=" C VAL N 64 " ideal model delta sigma weight residual 113.71 109.87 3.84 9.50e-01 1.11e+00 1.63e+01 angle pdb=" C ASN G 24 " pdb=" CA ASN G 24 " pdb=" CB ASN G 24 " ideal model delta sigma weight residual 111.68 117.96 -6.28 1.68e+00 3.54e-01 1.40e+01 angle pdb=" CA ASN G 24 " pdb=" CB ASN G 24 " pdb=" CG ASN G 24 " ideal model delta sigma weight residual 112.60 115.83 -3.23 1.00e+00 1.00e+00 1.04e+01 angle pdb=" O1 MAE R 401 " pdb=" C1 MAE R 401 " pdb=" O2 MAE R 401 " ideal model delta sigma weight residual 127.57 118.72 8.85 3.00e+00 1.11e-01 8.70e+00 ... (remaining 13711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 5371 17.92 - 35.84: 459 35.84 - 53.76: 139 53.76 - 71.68: 26 71.68 - 89.61: 12 Dihedral angle restraints: 6007 sinusoidal: 2318 harmonic: 3689 Sorted by residual: dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 159.53 20.47 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA ARG S 191 " pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta harmonic sigma weight residual 180.00 160.93 19.07 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA GLY B 162 " pdb=" C GLY B 162 " pdb=" N ASP B 163 " pdb=" CA ASP B 163 " ideal model delta harmonic sigma weight residual 180.00 161.15 18.85 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 6004 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1160 0.041 - 0.082: 289 0.082 - 0.122: 104 0.122 - 0.163: 13 0.163 - 0.204: 1 Chirality restraints: 1567 Sorted by residual: chirality pdb=" CA ASN G 24 " pdb=" N ASN G 24 " pdb=" C ASN G 24 " pdb=" CB ASN G 24 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ASN A 371 " pdb=" N ASN A 371 " pdb=" C ASN A 371 " pdb=" CB ASN A 371 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CA PRO N 102 " pdb=" N PRO N 102 " pdb=" C PRO N 102 " pdb=" CB PRO N 102 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 1564 not shown) Planarity restraints: 1742 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 46 " 0.157 9.50e-02 1.11e+02 7.06e-02 3.72e+00 pdb=" NE ARG B 46 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG B 46 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 46 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 46 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 209 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO R 210 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO R 210 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 210 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 24 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.91e+00 pdb=" C ASN G 24 " -0.024 2.00e-02 2.50e+03 pdb=" O ASN G 24 " 0.009 2.00e-02 2.50e+03 pdb=" N ILE G 25 " 0.008 2.00e-02 2.50e+03 ... (remaining 1739 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1271 2.75 - 3.29: 9690 3.29 - 3.82: 16923 3.82 - 4.36: 20908 4.36 - 4.90: 36179 Nonbonded interactions: 84971 Sorted by model distance: nonbonded pdb=" OG SER G 31 " pdb=" OD2 ASP B 27 " model vdw 2.212 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.245 3.040 nonbonded pdb=" NZ LYS R 32 " pdb=" OE2 GLU R 97 " model vdw 2.268 3.120 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.271 3.040 nonbonded pdb=" O THR G 52 " pdb=" OG1 THR G 52 " model vdw 2.282 3.040 ... (remaining 84966 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: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.160 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:8.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.195 10118 Z= 0.205 Angle : 0.582 8.851 13718 Z= 0.326 Chirality : 0.041 0.204 1567 Planarity : 0.004 0.071 1742 Dihedral : 15.597 89.605 3622 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.18 % Allowed : 16.90 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.24), residues: 1250 helix: 1.99 (0.26), residues: 404 sheet: 0.30 (0.28), residues: 336 loop : 0.35 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 46 TYR 0.015 0.001 TYR R 82 PHE 0.013 0.001 PHE R 127 TRP 0.012 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (10117) covalent geometry : angle 0.57893 / 0.33 (13716) SS BOND : bond 0.19459 / 10.24 ( 1) SS BOND : angle 5.00324 / 2.64 ( 2) hydrogen bonds : bond 0.16457 / 10.77 ( 510) hydrogen bonds : angle 6.84277 / 4.76 ( 1404) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 250 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7378 (mt-10) REVERT: A 28 LYS cc_start: 0.7972 (ttpt) cc_final: 0.7570 (mtmm) REVERT: A 213 GLN cc_start: 0.8901 (tt0) cc_final: 0.8646 (tt0) REVERT: A 295 ASP cc_start: 0.7810 (m-30) cc_final: 0.7606 (p0) REVERT: A 299 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7738 (mm-30) REVERT: A 343 LYS cc_start: 0.8315 (tttt) cc_final: 0.7991 (ttpt) REVERT: A 368 ASP cc_start: 0.7117 (t0) cc_final: 0.6891 (t70) REVERT: G 20 LYS cc_start: 0.8469 (mtmt) cc_final: 0.8145 (mppt) REVERT: G 38 MET cc_start: 0.7765 (ttp) cc_final: 0.7555 (ttp) REVERT: G 42 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7840 (pp20) REVERT: N 87 LYS cc_start: 0.7851 (mtpt) cc_final: 0.7590 (mttt) REVERT: R 276 ILE cc_start: 0.8516 (mm) cc_final: 0.8289 (pt) REVERT: R 281 HIS cc_start: 0.8239 (t70) cc_final: 0.7987 (t70) REVERT: S 109 ASP cc_start: 0.8599 (p0) cc_final: 0.8360 (p0) outliers start: 2 outliers final: 4 residues processed: 251 average time/residue: 0.5570 time to fit residues: 149.8986 Evaluate side-chains 188 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 184 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 176 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS A 294 GLN N 77 ASN R 279 GLN R 294 ASN B 17 GLN B 36 ASN B 239 ASN ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.144043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.103433 restraints weight = 12629.767| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.24 r_work: 0.3055 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10118 Z= 0.146 Angle : 0.554 7.945 13718 Z= 0.296 Chirality : 0.043 0.157 1567 Planarity : 0.004 0.039 1742 Dihedral : 5.118 49.122 1387 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.88 % Allowed : 17.27 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.24), residues: 1250 helix: 2.43 (0.26), residues: 401 sheet: 0.33 (0.29), residues: 312 loop : 0.40 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 38 TYR 0.019 0.002 TYR R 92 PHE 0.013 0.001 PHE A 212 TRP 0.021 0.002 TRP B 169 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (10117) covalent geometry : angle 0.55379 / 0.30 (13716) SS BOND : bond 0.00025 / 0.01 ( 1) SS BOND : angle 0.03521 / 0.02 ( 2) hydrogen bonds : bond 0.04311 / 2.82 ( 510) hydrogen bonds : angle 4.90953 / 3.45 ( 1404) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 204 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7831 (mt-10) REVERT: A 28 LYS cc_start: 0.8433 (ttpt) cc_final: 0.8046 (mtmm) REVERT: A 213 GLN cc_start: 0.9084 (tt0) cc_final: 0.8849 (tt0) REVERT: A 295 ASP cc_start: 0.8280 (m-30) cc_final: 0.7890 (p0) REVERT: A 299 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7723 (mm-30) REVERT: A 343 LYS cc_start: 0.8783 (tttt) cc_final: 0.8444 (ptmm) REVERT: G 20 LYS cc_start: 0.8458 (mtmt) cc_final: 0.8118 (mppt) REVERT: G 38 MET cc_start: 0.8092 (ttp) cc_final: 0.7803 (ttp) REVERT: G 58 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8101 (pm20) REVERT: N 7 SER cc_start: 0.8101 (p) cc_final: 0.7897 (m) REVERT: N 83 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8552 (mtp) REVERT: R 32 LYS cc_start: 0.7741 (mttt) cc_final: 0.7166 (mppt) REVERT: R 33 MET cc_start: 0.7594 (ttp) cc_final: 0.7346 (tpt) REVERT: R 97 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7699 (mm-30) REVERT: S 238 THR cc_start: 0.9017 (m) cc_final: 0.8694 (p) outliers start: 42 outliers final: 24 residues processed: 230 average time/residue: 0.5508 time to fit residues: 135.9701 Evaluate side-chains 216 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 176 ASN Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 244 ILE Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 94 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 GLN A 220 HIS A 294 GLN ** R 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 279 GLN B 17 GLN S 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.141644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.100914 restraints weight = 12621.449| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.21 r_work: 0.3018 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10118 Z= 0.185 Angle : 0.560 7.969 13718 Z= 0.295 Chirality : 0.043 0.157 1567 Planarity : 0.004 0.030 1742 Dihedral : 5.104 49.733 1385 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.52 % Allowed : 16.34 % Favored : 79.13 % 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 are not related in a simple way. whole: 1.38 (0.24), residues: 1250 helix: 2.41 (0.25), residues: 401 sheet: 0.17 (0.28), residues: 322 loop : 0.34 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 38 TYR 0.015 0.002 TYR R 92 PHE 0.014 0.002 PHE A 238 TRP 0.017 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (10117) covalent geometry : angle 0.55958 / 0.30 (13716) SS BOND : bond 0.00278 / 0.15 ( 1) SS BOND : angle 0.28647 / 0.16 ( 2) hydrogen bonds : bond 0.04296 / 2.81 ( 510) hydrogen bonds : angle 4.67485 / 3.29 ( 1404) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 195 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8047 (mtmm) REVERT: A 213 GLN cc_start: 0.9119 (tt0) cc_final: 0.8863 (tt0) REVERT: A 280 ARG cc_start: 0.8496 (ttt180) cc_final: 0.8083 (tpt-90) REVERT: A 295 ASP cc_start: 0.8308 (m-30) cc_final: 0.8102 (OUTLIER) REVERT: A 299 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7758 (mm-30) REVERT: A 343 LYS cc_start: 0.8796 (tttt) cc_final: 0.8437 (ptmm) REVERT: A 370 GLU cc_start: 0.8022 (mp0) cc_final: 0.7794 (mp0) REVERT: G 20 LYS cc_start: 0.8514 (mtmt) cc_final: 0.7963 (mppt) REVERT: G 38 MET cc_start: 0.8130 (ttp) cc_final: 0.7864 (ttp) REVERT: G 58 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8098 (pm20) REVERT: N 3 GLN cc_start: 0.8205 (tt0) cc_final: 0.7842 (tt0) REVERT: N 7 SER cc_start: 0.8093 (p) cc_final: 0.7875 (m) REVERT: N 83 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8721 (mtp) REVERT: R 32 LYS cc_start: 0.7765 (mttt) cc_final: 0.7177 (mppt) REVERT: R 42 ILE cc_start: 0.8414 (mt) cc_final: 0.8129 (mp) REVERT: R 97 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7923 (mm-30) REVERT: B 96 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8555 (mtt-85) REVERT: S 145 SER cc_start: 0.7720 (m) cc_final: 0.7112 (t) REVERT: S 238 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8696 (p) REVERT: S 244 LYS cc_start: 0.7654 (ttpp) cc_final: 0.7359 (tppt) outliers start: 49 outliers final: 33 residues processed: 221 average time/residue: 0.5811 time to fit residues: 137.9414 Evaluate side-chains 213 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 175 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 92 TYR Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 176 ASN Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 244 ILE Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 22 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 51 optimal weight: 0.0570 chunk 60 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 1 optimal weight: 0.4980 chunk 90 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS A 294 GLN ** R 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 279 GLN S 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.140132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.099624 restraints weight = 12397.492| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.21 r_work: 0.3057 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10118 Z= 0.133 Angle : 0.530 7.574 13718 Z= 0.276 Chirality : 0.042 0.155 1567 Planarity : 0.003 0.030 1742 Dihedral : 4.882 48.659 1384 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.97 % Allowed : 17.82 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.24), residues: 1250 helix: 2.45 (0.25), residues: 398 sheet: 0.18 (0.28), residues: 311 loop : 0.26 (0.28), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 38 TYR 0.018 0.001 TYR R 92 PHE 0.012 0.001 PHE A 212 TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (10117) covalent geometry : angle 0.53044 / 0.28 (13716) SS BOND : bond 0.00267 / 0.14 ( 1) SS BOND : angle 0.39222 / 0.21 ( 2) hydrogen bonds : bond 0.03857 / 2.53 ( 510) hydrogen bonds : angle 4.52844 / 3.18 ( 1404) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 193 time to evaluate : 0.497 Fit side-chains REVERT: A 28 LYS cc_start: 0.8449 (ttpt) cc_final: 0.8057 (mtmm) REVERT: A 213 GLN cc_start: 0.9150 (tt0) cc_final: 0.8904 (tt0) REVERT: A 280 ARG cc_start: 0.8440 (ttt180) cc_final: 0.8057 (tpt-90) REVERT: A 299 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7792 (mm-30) REVERT: A 343 LYS cc_start: 0.8846 (tttt) cc_final: 0.8525 (ptmm) REVERT: A 370 GLU cc_start: 0.8187 (mp0) cc_final: 0.7872 (mp0) REVERT: G 20 LYS cc_start: 0.8435 (mtmt) cc_final: 0.8017 (mppt) REVERT: G 38 MET cc_start: 0.8133 (ttp) cc_final: 0.7864 (ttp) REVERT: G 58 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8082 (pm20) REVERT: N 3 GLN cc_start: 0.8261 (tt0) cc_final: 0.7905 (tt0) REVERT: N 7 SER cc_start: 0.8138 (p) cc_final: 0.7914 (m) REVERT: N 58 ILE cc_start: 0.8929 (pt) cc_final: 0.8504 (mt) REVERT: N 83 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8735 (mtp) REVERT: R 32 LYS cc_start: 0.7806 (mttt) cc_final: 0.7347 (mtmt) REVERT: R 42 ILE cc_start: 0.8433 (mt) cc_final: 0.8094 (mp) REVERT: R 90 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.7954 (pp) REVERT: R 97 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.8028 (mm-30) REVERT: B 96 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8540 (mtt-85) REVERT: S 18 ARG cc_start: 0.7884 (tpp80) cc_final: 0.7673 (tpp80) REVERT: S 145 SER cc_start: 0.7792 (m) cc_final: 0.7207 (t) REVERT: S 238 THR cc_start: 0.9067 (OUTLIER) cc_final: 0.8774 (p) REVERT: S 244 LYS cc_start: 0.7792 (ttpp) cc_final: 0.7507 (tppt) outliers start: 43 outliers final: 27 residues processed: 219 average time/residue: 0.6145 time to fit residues: 144.1634 Evaluate side-chains 211 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 90 ILE Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 244 ILE Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 41 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 11 optimal weight: 0.0570 chunk 108 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 122 optimal weight: 8.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS A 294 GLN ** R 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 279 GLN S 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.141940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.104534 restraints weight = 12446.229| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.15 r_work: 0.3102 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10118 Z= 0.107 Angle : 0.500 6.749 13718 Z= 0.262 Chirality : 0.040 0.136 1567 Planarity : 0.003 0.033 1742 Dihedral : 4.488 46.898 1382 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.97 % Allowed : 18.37 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.24), residues: 1250 helix: 2.50 (0.26), residues: 399 sheet: 0.15 (0.27), residues: 333 loop : 0.34 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 38 TYR 0.014 0.001 TYR S 190 PHE 0.011 0.001 PHE A 212 TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (10117) covalent geometry : angle 0.50043 / 0.26 (13716) SS BOND : bond 0.00368 / 0.19 ( 1) SS BOND : angle 0.40253 / 0.21 ( 2) hydrogen bonds : bond 0.03473 / 2.29 ( 510) hydrogen bonds : angle 4.31950 / 3.04 ( 1404) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 197 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8427 (ttpt) cc_final: 0.8103 (mtmm) REVERT: A 213 GLN cc_start: 0.9148 (tt0) cc_final: 0.8927 (tt0) REVERT: A 299 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7809 (mm-30) REVERT: A 307 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7158 (mtmm) REVERT: A 343 LYS cc_start: 0.8874 (tttt) cc_final: 0.8587 (ptmm) REVERT: A 370 GLU cc_start: 0.8210 (mp0) cc_final: 0.7802 (mp0) REVERT: A 378 ASP cc_start: 0.8757 (m-30) cc_final: 0.8547 (m-30) REVERT: G 18 GLN cc_start: 0.7978 (tp40) cc_final: 0.7719 (tp-100) REVERT: G 20 LYS cc_start: 0.8533 (mtmt) cc_final: 0.8200 (mtmm) REVERT: G 38 MET cc_start: 0.8146 (ttp) cc_final: 0.7890 (ttp) REVERT: N 3 GLN cc_start: 0.8336 (tt0) cc_final: 0.7980 (tt0) REVERT: N 7 SER cc_start: 0.8135 (p) cc_final: 0.7885 (m) REVERT: N 58 ILE cc_start: 0.8873 (pt) cc_final: 0.8568 (mt) REVERT: N 83 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8753 (mtp) REVERT: R 32 LYS cc_start: 0.7864 (mttt) cc_final: 0.7662 (mtmp) REVERT: R 42 ILE cc_start: 0.8438 (mt) cc_final: 0.8199 (mp) REVERT: S 145 SER cc_start: 0.7756 (m) cc_final: 0.7250 (t) REVERT: S 238 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8806 (p) REVERT: S 244 LYS cc_start: 0.7844 (ttpp) cc_final: 0.7484 (tmtt) outliers start: 43 outliers final: 29 residues processed: 219 average time/residue: 0.6125 time to fit residues: 143.4794 Evaluate side-chains 212 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 176 ASN Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 244 ILE Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 113 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 120 optimal weight: 20.0000 chunk 85 optimal weight: 0.1980 chunk 38 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS R 279 GLN R 294 ASN S 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.142598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.106641 restraints weight = 12457.431| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.07 r_work: 0.3112 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10118 Z= 0.110 Angle : 0.512 7.680 13718 Z= 0.265 Chirality : 0.041 0.147 1567 Planarity : 0.003 0.033 1742 Dihedral : 4.434 46.740 1382 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.97 % Allowed : 19.11 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.24), residues: 1250 helix: 2.49 (0.26), residues: 400 sheet: 0.20 (0.27), residues: 333 loop : 0.33 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 317 TYR 0.018 0.001 TYR R 92 PHE 0.012 0.001 PHE A 212 TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (10117) covalent geometry : angle 0.51169 / 0.27 (13716) SS BOND : bond 0.00420 / 0.22 ( 1) SS BOND : angle 0.47604 / 0.26 ( 2) hydrogen bonds : bond 0.03468 / 2.28 ( 510) hydrogen bonds : angle 4.25520 / 2.99 ( 1404) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 192 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8473 (ttpt) cc_final: 0.8125 (mtmm) REVERT: A 213 GLN cc_start: 0.9130 (tt0) cc_final: 0.8920 (tt0) REVERT: A 299 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7861 (mm-30) REVERT: A 314 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7451 (mp0) REVERT: A 343 LYS cc_start: 0.8913 (tttt) cc_final: 0.8651 (ptmm) REVERT: A 370 GLU cc_start: 0.8253 (mp0) cc_final: 0.7858 (mp0) REVERT: A 378 ASP cc_start: 0.8735 (m-30) cc_final: 0.8506 (m-30) REVERT: G 20 LYS cc_start: 0.8510 (mtmt) cc_final: 0.8055 (mppt) REVERT: G 38 MET cc_start: 0.8214 (ttp) cc_final: 0.7965 (ttp) REVERT: G 58 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8040 (pm20) REVERT: N 3 GLN cc_start: 0.8336 (tt0) cc_final: 0.8002 (tt0) REVERT: N 7 SER cc_start: 0.8130 (p) cc_final: 0.7883 (m) REVERT: N 58 ILE cc_start: 0.8901 (pt) cc_final: 0.8628 (mp) REVERT: N 83 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8775 (mtp) REVERT: R 32 LYS cc_start: 0.7977 (mttt) cc_final: 0.7763 (mtmp) REVERT: R 192 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7646 (tt) REVERT: B 130 GLU cc_start: 0.9024 (mp0) cc_final: 0.8676 (mp0) REVERT: S 18 ARG cc_start: 0.8091 (tpp80) cc_final: 0.7882 (tpp80) REVERT: S 145 SER cc_start: 0.7906 (m) cc_final: 0.7410 (t) REVERT: S 238 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8837 (p) REVERT: S 244 LYS cc_start: 0.7939 (ttpp) cc_final: 0.7607 (tmtt) outliers start: 43 outliers final: 27 residues processed: 213 average time/residue: 0.5612 time to fit residues: 128.2560 Evaluate side-chains 212 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 90 ILE Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 176 ASN Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 244 ILE Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 26 optimal weight: 0.0870 chunk 73 optimal weight: 6.9990 chunk 63 optimal weight: 0.0770 chunk 11 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 14 optimal weight: 0.0670 chunk 0 optimal weight: 6.9990 overall best weight: 0.3654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS G 18 GLN R 279 GLN S 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.147616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.112127 restraints weight = 12697.115| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.17 r_work: 0.3117 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10118 Z= 0.095 Angle : 0.500 7.924 13718 Z= 0.259 Chirality : 0.040 0.141 1567 Planarity : 0.003 0.032 1742 Dihedral : 4.290 45.330 1382 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.68 % Allowed : 20.04 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.24), residues: 1250 helix: 2.56 (0.26), residues: 397 sheet: 0.48 (0.28), residues: 316 loop : 0.22 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 317 TYR 0.012 0.001 TYR S 190 PHE 0.011 0.001 PHE A 212 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 (10117) covalent geometry : angle 0.49979 / 0.26 (13716) SS BOND : bond 0.00400 / 0.21 ( 1) SS BOND : angle 0.44880 / 0.24 ( 2) hydrogen bonds : bond 0.03220 / 2.14 ( 510) hydrogen bonds : angle 4.13829 / 2.91 ( 1404) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 203 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8453 (ttpt) cc_final: 0.8110 (mtmm) REVERT: A 213 GLN cc_start: 0.9116 (tt0) cc_final: 0.8875 (tt0) REVERT: A 299 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7764 (mm-30) REVERT: A 343 LYS cc_start: 0.8840 (tttt) cc_final: 0.8270 (ptmm) REVERT: A 370 GLU cc_start: 0.8144 (mp0) cc_final: 0.7605 (mp0) REVERT: A 378 ASP cc_start: 0.8664 (m-30) cc_final: 0.8377 (m-30) REVERT: G 20 LYS cc_start: 0.8527 (mtmt) cc_final: 0.8203 (mtmm) REVERT: G 38 MET cc_start: 0.8048 (ttp) cc_final: 0.7789 (ttp) REVERT: N 3 GLN cc_start: 0.8314 (tt0) cc_final: 0.7960 (tt0) REVERT: N 7 SER cc_start: 0.8060 (p) cc_final: 0.7785 (m) REVERT: N 58 ILE cc_start: 0.8848 (pt) cc_final: 0.8616 (mp) REVERT: N 83 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8733 (mtp) REVERT: R 32 LYS cc_start: 0.7956 (mttt) cc_final: 0.7714 (mtmp) REVERT: R 197 TRP cc_start: 0.8442 (m100) cc_final: 0.7185 (m-10) REVERT: B 32 GLN cc_start: 0.8305 (mt0) cc_final: 0.7926 (mt0) REVERT: B 48 ARG cc_start: 0.8799 (mmt180) cc_final: 0.8574 (mmm160) REVERT: B 130 GLU cc_start: 0.8982 (mp0) cc_final: 0.8629 (mp0) REVERT: B 134 ARG cc_start: 0.8306 (ptp90) cc_final: 0.7869 (ptm-80) REVERT: S 18 ARG cc_start: 0.8059 (tpp80) cc_final: 0.7825 (tpp80) REVERT: S 145 SER cc_start: 0.7900 (m) cc_final: 0.7333 (t) REVERT: S 238 THR cc_start: 0.9045 (OUTLIER) cc_final: 0.8801 (p) REVERT: S 244 LYS cc_start: 0.7881 (ttpp) cc_final: 0.7516 (tmtt) outliers start: 29 outliers final: 22 residues processed: 218 average time/residue: 0.5418 time to fit residues: 126.5725 Evaluate side-chains 210 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 176 ASN Chi-restraints excluded: chain R residue 244 ILE Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 59 optimal weight: 0.3980 chunk 62 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS N 31 ASN R 279 GLN S 39 GLN S 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.145103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.105749 restraints weight = 12553.808| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.20 r_work: 0.3096 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10118 Z= 0.112 Angle : 0.527 9.505 13718 Z= 0.271 Chirality : 0.041 0.177 1567 Planarity : 0.003 0.036 1742 Dihedral : 4.363 44.971 1382 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.95 % Allowed : 20.13 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.24), residues: 1250 helix: 2.50 (0.26), residues: 395 sheet: 0.35 (0.27), residues: 328 loop : 0.32 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 317 TYR 0.018 0.001 TYR R 92 PHE 0.022 0.001 PHE R 104 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (10117) covalent geometry : angle 0.52712 / 0.27 (13716) SS BOND : bond 0.00414 / 0.22 ( 1) SS BOND : angle 0.50679 / 0.28 ( 2) hydrogen bonds : bond 0.03360 / 2.22 ( 510) hydrogen bonds : angle 4.17404 / 2.93 ( 1404) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8415 (ttpt) cc_final: 0.8065 (mtmm) REVERT: A 213 GLN cc_start: 0.9112 (tt0) cc_final: 0.8866 (tt0) REVERT: A 299 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7761 (mm-30) REVERT: A 314 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: A 343 LYS cc_start: 0.8702 (tttt) cc_final: 0.8392 (ptmm) REVERT: A 370 GLU cc_start: 0.8148 (mp0) cc_final: 0.7560 (mp0) REVERT: A 378 ASP cc_start: 0.8676 (m-30) cc_final: 0.8399 (m-30) REVERT: G 18 GLN cc_start: 0.7843 (tp40) cc_final: 0.7600 (tp-100) REVERT: G 20 LYS cc_start: 0.8384 (mtmt) cc_final: 0.7941 (mppt) REVERT: G 38 MET cc_start: 0.8024 (ttp) cc_final: 0.7737 (ttp) REVERT: N 3 GLN cc_start: 0.8279 (tt0) cc_final: 0.7906 (tt0) REVERT: N 7 SER cc_start: 0.8064 (p) cc_final: 0.7803 (m) REVERT: N 58 ILE cc_start: 0.8818 (pt) cc_final: 0.8581 (mp) REVERT: N 83 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8682 (mtp) REVERT: R 32 LYS cc_start: 0.7937 (mttt) cc_final: 0.7655 (mtmp) REVERT: R 197 TRP cc_start: 0.8458 (m100) cc_final: 0.7207 (m-10) REVERT: B 32 GLN cc_start: 0.8277 (mt0) cc_final: 0.7970 (mt0) REVERT: B 48 ARG cc_start: 0.8816 (mmt180) cc_final: 0.8548 (mmm160) REVERT: B 134 ARG cc_start: 0.8302 (ptp90) cc_final: 0.7883 (ptm-80) REVERT: S 238 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8808 (p) REVERT: S 244 LYS cc_start: 0.7871 (ttpp) cc_final: 0.7481 (tmtt) outliers start: 32 outliers final: 25 residues processed: 206 average time/residue: 0.5687 time to fit residues: 125.3611 Evaluate side-chains 212 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 90 ILE Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 176 ASN Chi-restraints excluded: chain R residue 244 ILE Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 39 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 35 optimal weight: 0.3980 chunk 50 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS N 31 ASN R 279 GLN S 39 GLN S 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.141656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.101752 restraints weight = 12367.592| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.21 r_work: 0.3078 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10118 Z= 0.126 Angle : 0.551 10.111 13718 Z= 0.283 Chirality : 0.042 0.194 1567 Planarity : 0.003 0.036 1742 Dihedral : 4.433 44.506 1382 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.95 % Allowed : 21.05 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.24), residues: 1250 helix: 2.43 (0.26), residues: 397 sheet: 0.32 (0.28), residues: 328 loop : 0.36 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 317 TYR 0.013 0.001 TYR N 32 PHE 0.014 0.001 PHE R 296 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (10117) covalent geometry : angle 0.55090 / 0.28 (13716) SS BOND : bond 0.00427 / 0.22 ( 1) SS BOND : angle 0.55900 / 0.30 ( 2) hydrogen bonds : bond 0.03494 / 2.31 ( 510) hydrogen bonds : angle 4.23446 / 2.98 ( 1404) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8418 (ttpt) cc_final: 0.8047 (mtmm) REVERT: A 213 GLN cc_start: 0.9125 (tt0) cc_final: 0.8879 (tt0) REVERT: A 299 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7738 (mm-30) REVERT: A 314 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: A 330 GLU cc_start: 0.8099 (tt0) cc_final: 0.7878 (tt0) REVERT: A 343 LYS cc_start: 0.8714 (tttt) cc_final: 0.8390 (ptmm) REVERT: A 370 GLU cc_start: 0.8171 (mp0) cc_final: 0.7686 (mp0) REVERT: A 378 ASP cc_start: 0.8691 (m-30) cc_final: 0.8428 (m-30) REVERT: G 38 MET cc_start: 0.8048 (ttp) cc_final: 0.7755 (ttp) REVERT: N 3 GLN cc_start: 0.8293 (tt0) cc_final: 0.7902 (tt0) REVERT: N 7 SER cc_start: 0.8087 (p) cc_final: 0.7828 (m) REVERT: N 58 ILE cc_start: 0.8854 (pt) cc_final: 0.8616 (mp) REVERT: N 83 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8711 (mtp) REVERT: R 32 LYS cc_start: 0.7905 (mttt) cc_final: 0.7681 (mtmp) REVERT: B 32 GLN cc_start: 0.8305 (mt0) cc_final: 0.7996 (mt0) REVERT: B 130 GLU cc_start: 0.9023 (mp0) cc_final: 0.8630 (mp0) REVERT: B 134 ARG cc_start: 0.8333 (ptp90) cc_final: 0.7869 (ptm-80) REVERT: S 238 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8795 (p) REVERT: S 244 LYS cc_start: 0.7883 (ttpp) cc_final: 0.7476 (tmtt) outliers start: 32 outliers final: 24 residues processed: 194 average time/residue: 0.5909 time to fit residues: 122.4161 Evaluate side-chains 199 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 90 ILE Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 244 ILE Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 32 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS A 294 GLN G 18 GLN R 279 GLN S 39 GLN S 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.140679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.103137 restraints weight = 12235.595| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.16 r_work: 0.3066 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10118 Z= 0.153 Angle : 0.582 10.758 13718 Z= 0.299 Chirality : 0.042 0.190 1567 Planarity : 0.004 0.040 1742 Dihedral : 4.558 44.437 1382 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.95 % Allowed : 21.33 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.24), residues: 1250 helix: 2.36 (0.26), residues: 394 sheet: 0.35 (0.28), residues: 312 loop : 0.21 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 317 TYR 0.016 0.001 TYR R 92 PHE 0.022 0.002 PHE R 104 TRP 0.013 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (10117) covalent geometry : angle 0.58163 / 0.30 (13716) SS BOND : bond 0.00322 / 0.17 ( 1) SS BOND : angle 0.40180 / 0.23 ( 2) hydrogen bonds : bond 0.03755 / 2.48 ( 510) hydrogen bonds : angle 4.33129 / 3.05 ( 1404) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.397 Fit side-chains REVERT: A 28 LYS cc_start: 0.8511 (ttpt) cc_final: 0.8132 (mtmm) REVERT: A 213 GLN cc_start: 0.9148 (tt0) cc_final: 0.8912 (tt0) REVERT: A 299 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7824 (mm-30) REVERT: A 314 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7453 (mp0) REVERT: A 330 GLU cc_start: 0.8186 (tt0) cc_final: 0.7748 (tt0) REVERT: A 343 LYS cc_start: 0.8843 (tttt) cc_final: 0.8530 (ptmm) REVERT: A 370 GLU cc_start: 0.8278 (mp0) cc_final: 0.7816 (mp0) REVERT: A 378 ASP cc_start: 0.8725 (m-30) cc_final: 0.8506 (m-30) REVERT: G 38 MET cc_start: 0.8218 (ttp) cc_final: 0.7919 (ttp) REVERT: N 3 GLN cc_start: 0.8379 (tt0) cc_final: 0.7983 (tt0) REVERT: N 7 SER cc_start: 0.8129 (p) cc_final: 0.7888 (m) REVERT: N 58 ILE cc_start: 0.8964 (pt) cc_final: 0.8738 (mt) REVERT: N 83 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8771 (mtp) REVERT: R 32 LYS cc_start: 0.8059 (mttt) cc_final: 0.7804 (mtmp) REVERT: R 307 ASP cc_start: 0.8634 (m-30) cc_final: 0.8389 (m-30) REVERT: B 32 GLN cc_start: 0.8383 (mt0) cc_final: 0.8048 (mt0) REVERT: B 130 GLU cc_start: 0.9090 (mp0) cc_final: 0.8658 (mp0) REVERT: S 18 ARG cc_start: 0.7939 (tpp80) cc_final: 0.7596 (tpp80) outliers start: 32 outliers final: 28 residues processed: 193 average time/residue: 0.5991 time to fit residues: 123.2887 Evaluate side-chains 200 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 90 ILE Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 244 ILE Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain R residue 305 VAL Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 47 optimal weight: 0.8980 chunk 85 optimal weight: 0.0770 chunk 22 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 109 optimal weight: 6.9990 chunk 38 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS A 294 GLN R 279 GLN S 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.143514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.104205 restraints weight = 12394.859| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.20 r_work: 0.3079 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10118 Z= 0.109 Angle : 0.555 11.077 13718 Z= 0.282 Chirality : 0.041 0.184 1567 Planarity : 0.003 0.039 1742 Dihedral : 4.393 42.310 1382 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.68 % Allowed : 21.88 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.24), residues: 1250 helix: 2.41 (0.26), residues: 394 sheet: 0.31 (0.28), residues: 328 loop : 0.30 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 317 TYR 0.011 0.001 TYR S 190 PHE 0.020 0.001 PHE R 296 TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (10117) covalent geometry : angle 0.55486 / 0.28 (13716) SS BOND : bond 0.00411 / 0.22 ( 1) SS BOND : angle 0.49223 / 0.26 ( 2) hydrogen bonds : bond 0.03393 / 2.25 ( 510) hydrogen bonds : angle 4.21085 / 2.96 ( 1404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4320.06 seconds wall clock time: 74 minutes 20.18 seconds (4460.18 seconds total)