Starting phenix.real_space_refine on Thu Jan 16 17:38:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zx1_60536/01_2025/8zx1_60536.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zx1_60536/01_2025/8zx1_60536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zx1_60536/01_2025/8zx1_60536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zx1_60536/01_2025/8zx1_60536.map" model { file = "/net/cci-nas-00/data/ceres_data/8zx1_60536/01_2025/8zx1_60536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zx1_60536/01_2025/8zx1_60536.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.044 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 60 5.16 5 C 6381 2.51 5 N 1644 2.21 5 O 1761 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 9846 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2876 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 14, 'TRANS': 345} Chain: "B" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2172 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 15, 'TRANS': 257} Chain: "C" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1936 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 9, 'TRANS': 239} Chain: "D" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2862 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 13, 'TRANS': 344} Time building chain proxies: 5.71, per 1000 atoms: 0.58 Number of scatterers: 9846 At special positions: 0 Unit cell: (85.36, 96.03, 132.89, 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 60 16.00 O 1761 8.00 N 1644 7.00 C 6381 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.4 seconds 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2332 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 9 sheets defined 51.9% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 55 through 65 Processing helix chain 'A' and resid 105 through 117 removed outlier: 5.049A pdb=" N GLY A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 135 removed outlier: 3.639A pdb=" N ILE A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) Proline residue: A 126 - end of helix removed outlier: 3.700A pdb=" N VAL A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 163 Processing helix chain 'A' and resid 179 through 198 removed outlier: 3.684A pdb=" N ASN A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 removed outlier: 3.553A pdb=" N ALA A 211 " --> pdb=" O ASP A 207 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 238 removed outlier: 3.606A pdb=" N GLU A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'B' and resid 8 through 23 removed outlier: 4.247A pdb=" N ILE B 12 " --> pdb=" O GLN B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 32 removed outlier: 3.510A pdb=" N MET B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 55 removed outlier: 3.848A pdb=" N THR B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG B 55 " --> pdb=" O ASP B 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 50 through 55' Processing helix chain 'B' and resid 58 through 91 removed outlier: 4.029A pdb=" N VAL B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU B 65 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET B 71 " --> pdb=" O HIS B 67 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 75 " --> pdb=" O MET B 71 " (cutoff:3.500A) Proline residue: B 85 - end of helix Processing helix chain 'B' and resid 97 through 104 Processing helix chain 'B' and resid 105 through 111 Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 112 through 124 removed outlier: 3.585A pdb=" N TYR B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 122 " --> pdb=" O TYR B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 137 Processing helix chain 'B' and resid 149 through 162 removed outlier: 3.526A pdb=" N VAL B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 175 removed outlier: 3.556A pdb=" N VAL B 166 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET B 167 " --> pdb=" O PRO B 163 " (cutoff:3.500A) Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 177 through 188 removed outlier: 3.513A pdb=" N LEU B 181 " --> pdb=" O ASP B 177 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 198 Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 203 through 219 removed outlier: 3.580A pdb=" N VAL B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Proline residue: B 217 - end of helix Processing helix chain 'B' and resid 221 through 229 removed outlier: 4.495A pdb=" N SER B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 246 Processing helix chain 'B' and resid 249 through 279 removed outlier: 3.795A pdb=" N THR B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU B 260 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL B 263 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 30 removed outlier: 3.906A pdb=" N PHE C 10 " --> pdb=" O LEU C 6 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET C 11 " --> pdb=" O ARG C 7 " (cutoff:3.500A) Proline residue: C 21 - end of helix removed outlier: 3.693A pdb=" N PHE C 30 " --> pdb=" O ILE C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 52 removed outlier: 3.589A pdb=" N SER C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 88 Processing helix chain 'C' and resid 92 through 105 Processing helix chain 'C' and resid 107 through 123 Processing helix chain 'C' and resid 127 through 152 Proline residue: C 141 - end of helix Processing helix chain 'C' and resid 156 through 165 removed outlier: 4.263A pdb=" N GLU C 160 " --> pdb=" O VAL C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 176 removed outlier: 3.854A pdb=" N LEU C 173 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG C 174 " --> pdb=" O PHE C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 199 removed outlier: 3.726A pdb=" N LEU C 180 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Proline residue: C 183 - end of helix removed outlier: 3.642A pdb=" N MET C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP C 199 " --> pdb=" O LEU C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 207 removed outlier: 3.558A pdb=" N THR C 207 " --> pdb=" O SER C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 225 removed outlier: 4.188A pdb=" N LYS C 223 " --> pdb=" O TYR C 219 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL C 224 " --> pdb=" O SER C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 253 removed outlier: 3.645A pdb=" N THR C 235 " --> pdb=" O ASN C 231 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET C 244 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG C 253 " --> pdb=" O GLN C 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 65 Processing helix chain 'D' and resid 105 through 117 removed outlier: 4.798A pdb=" N GLY D 113 " --> pdb=" O ASN D 109 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 135 removed outlier: 3.907A pdb=" N ILE D 124 " --> pdb=" O PRO D 120 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N THR D 125 " --> pdb=" O ALA D 121 " (cutoff:3.500A) Proline residue: D 126 - end of helix removed outlier: 3.586A pdb=" N VAL D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 163 Processing helix chain 'D' and resid 181 through 198 removed outlier: 3.776A pdb=" N ASN D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 215 removed outlier: 3.632A pdb=" N ALA D 211 " --> pdb=" O ASP D 207 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER D 215 " --> pdb=" O ALA D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 238 Processing helix chain 'D' and resid 243 through 248 Processing helix chain 'D' and resid 295 through 297 No H-bonds generated for 'chain 'D' and resid 295 through 297' Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 41 removed outlier: 6.183A pdb=" N VAL A 32 " --> pdb=" O CYS A 26 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N CYS A 26 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ARG A 24 " --> pdb=" O PRO A 34 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU A 36 " --> pdb=" O GLY A 22 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY A 22 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU A 20 " --> pdb=" O MET A 75 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N MET A 75 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N GLY A 22 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ARG A 73 " --> pdb=" O GLY A 22 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 71 " --> pdb=" O ARG A 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.570A pdb=" N LEU A 169 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL A 204 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE A 45 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL A 219 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N THR A 47 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N MET A 221 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU A 49 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE A 218 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP A 229 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL A 220 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 274 through 278 removed outlier: 3.520A pdb=" N ALA A 269 " --> pdb=" O CYS A 276 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE A 278 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ARG A 268 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 256 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 370 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 299 through 303 removed outlier: 3.741A pdb=" N ALA A 361 " --> pdb=" O GLU A 302 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL A 330 " --> pdb=" O ARG A 318 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ARG A 320 " --> pdb=" O GLU A 328 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLU A 328 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N TYR A 322 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N THR A 326 " --> pdb=" O TYR A 322 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 30 through 40 removed outlier: 6.744A pdb=" N LYS D 25 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE D 23 " --> pdb=" O PRO D 34 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU D 36 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA D 21 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU D 38 " --> pdb=" O GLN D 19 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLN D 19 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE D 23 " --> pdb=" O SER D 71 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER D 71 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 91 through 94 removed outlier: 6.572A pdb=" N ASN D 92 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL D 204 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHE D 45 " --> pdb=" O ARG D 217 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N VAL D 219 " --> pdb=" O PHE D 45 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR D 47 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N MET D 221 " --> pdb=" O THR D 47 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU D 49 " --> pdb=" O MET D 221 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN D 228 " --> pdb=" O VAL D 220 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG D 222 " --> pdb=" O ILE D 226 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ILE D 226 " --> pdb=" O ARG D 222 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 274 through 279 removed outlier: 3.860A pdb=" N CYS D 276 " --> pdb=" O ALA D 269 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA D 269 " --> pdb=" O CYS D 276 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ARG D 266 " --> pdb=" O ARG D 261 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ARG D 261 " --> pdb=" O ARG D 266 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ARG D 268 " --> pdb=" O ILE D 259 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL D 370 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 299 through 303 Processing sheet with id=AA9, first strand: chain 'D' and resid 319 through 322 removed outlier: 4.270A pdb=" N GLU D 319 " --> pdb=" O VAL D 330 " (cutoff:3.500A) 466 hydrogen bonds defined for protein. 1365 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.78 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2168 1.33 - 1.45: 2106 1.45 - 1.58: 5656 1.58 - 1.70: 0 1.70 - 1.82: 111 Bond restraints: 10041 Sorted by residual: bond pdb=" N PHE D 95 " pdb=" CA PHE D 95 " ideal model delta sigma weight residual 1.454 1.490 -0.037 1.21e-02 6.83e+03 9.17e+00 bond pdb=" N VAL D 365 " pdb=" CA VAL D 365 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.20e-02 6.94e+03 8.19e+00 bond pdb=" N SER D 367 " pdb=" CA SER D 367 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.32e-02 5.74e+03 6.97e+00 bond pdb=" N GLU D 366 " pdb=" CA GLU D 366 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.28e-02 6.10e+03 6.86e+00 bond pdb=" N ASP D 351 " pdb=" CA ASP D 351 " ideal model delta sigma weight residual 1.457 1.487 -0.031 1.20e-02 6.94e+03 6.47e+00 ... (remaining 10036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.94: 13569 5.94 - 11.89: 41 11.89 - 17.83: 4 17.83 - 23.78: 1 23.78 - 29.72: 1 Bond angle restraints: 13616 Sorted by residual: angle pdb=" C ASN D 321 " pdb=" CA ASN D 321 " pdb=" CB ASN D 321 " ideal model delta sigma weight residual 110.74 81.02 29.72 1.61e+00 3.86e-01 3.41e+02 angle pdb=" N TYR D 322 " pdb=" CA TYR D 322 " pdb=" CB TYR D 322 " ideal model delta sigma weight residual 110.56 91.37 19.19 1.56e+00 4.11e-01 1.51e+02 angle pdb=" N TYR D 322 " pdb=" CA TYR D 322 " pdb=" C TYR D 322 " ideal model delta sigma weight residual 110.42 100.18 10.24 1.55e+00 4.16e-01 4.37e+01 angle pdb=" N ASN D 321 " pdb=" CA ASN D 321 " pdb=" C ASN D 321 " ideal model delta sigma weight residual 108.02 97.40 10.62 1.75e+00 3.27e-01 3.68e+01 angle pdb=" CB MET D 116 " pdb=" CG MET D 116 " pdb=" SD MET D 116 " ideal model delta sigma weight residual 112.70 96.99 15.71 3.00e+00 1.11e-01 2.74e+01 ... (remaining 13611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5442 17.94 - 35.89: 506 35.89 - 53.83: 77 53.83 - 71.77: 17 71.77 - 89.71: 8 Dihedral angle restraints: 6050 sinusoidal: 2450 harmonic: 3600 Sorted by residual: dihedral pdb=" C ASN D 321 " pdb=" N ASN D 321 " pdb=" CA ASN D 321 " pdb=" CB ASN D 321 " ideal model delta harmonic sigma weight residual -122.60 -83.26 -39.34 0 2.50e+00 1.60e-01 2.48e+02 dihedral pdb=" N TYR D 322 " pdb=" C TYR D 322 " pdb=" CA TYR D 322 " pdb=" CB TYR D 322 " ideal model delta harmonic sigma weight residual 122.80 95.21 27.59 0 2.50e+00 1.60e-01 1.22e+02 dihedral pdb=" C TYR D 322 " pdb=" N TYR D 322 " pdb=" CA TYR D 322 " pdb=" CB TYR D 322 " ideal model delta harmonic sigma weight residual -122.60 -110.50 -12.10 0 2.50e+00 1.60e-01 2.34e+01 ... (remaining 6047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 1540 0.125 - 0.249: 50 0.249 - 0.374: 5 0.374 - 0.499: 0 0.499 - 0.623: 2 Chirality restraints: 1597 Sorted by residual: chirality pdb=" CA TYR D 322 " pdb=" N TYR D 322 " pdb=" C TYR D 322 " pdb=" CB TYR D 322 " both_signs ideal model delta sigma weight residual False 2.51 3.13 -0.62 2.00e-01 2.50e+01 9.71e+00 chirality pdb=" CA ASN D 321 " pdb=" N ASN D 321 " pdb=" C ASN D 321 " pdb=" CB ASN D 321 " both_signs ideal model delta sigma weight residual False 2.51 3.12 -0.61 2.00e-01 2.50e+01 9.34e+00 chirality pdb=" CA PHE B 43 " pdb=" N PHE B 43 " pdb=" C PHE B 43 " pdb=" CB PHE B 43 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 ... (remaining 1594 not shown) Planarity restraints: 1723 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 101 " 0.022 2.00e-02 2.50e+03 2.52e-02 1.11e+01 pdb=" CG PHE C 101 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE C 101 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE C 101 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE C 101 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 101 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE C 101 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 110 " -0.025 2.00e-02 2.50e+03 2.06e-02 1.06e+01 pdb=" CG TRP B 110 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP B 110 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B 110 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 110 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 110 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 110 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 110 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 110 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 110 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 33 " -0.049 5.00e-02 4.00e+02 7.39e-02 8.74e+00 pdb=" N PRO D 34 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO D 34 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 34 " -0.040 5.00e-02 4.00e+02 ... (remaining 1720 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 66 2.52 - 3.11: 7631 3.11 - 3.71: 15023 3.71 - 4.30: 20424 4.30 - 4.90: 33709 Nonbonded interactions: 76853 Sorted by model distance: nonbonded pdb=" OG1 THR A 105 " pdb=" OE1 GLU A 108 " model vdw 1.921 3.040 nonbonded pdb=" OG SER C 227 " pdb=" OE1 GLU C 229 " model vdw 1.973 3.040 nonbonded pdb=" O PHE D 344 " pdb=" CZ PHE D 352 " model vdw 1.985 3.340 nonbonded pdb=" OD2 ASP C 155 " pdb=" NH1 ARG C 157 " model vdw 2.150 3.120 nonbonded pdb=" O PHE D 344 " pdb=" CE1 PHE D 352 " model vdw 2.181 3.340 ... (remaining 76848 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 16 through 373) selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.130 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5954 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 : 0.007 0.083 10041 Z= 0.437 Angle : 1.122 29.721 13616 Z= 0.610 Chirality : 0.063 0.623 1597 Planarity : 0.006 0.074 1723 Dihedral : 13.958 89.713 3718 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.01 % Allowed : 3.69 % Favored : 95.30 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.24), residues: 1232 helix: 0.94 (0.22), residues: 556 sheet: 0.25 (0.38), residues: 207 loop : -1.74 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP B 110 HIS 0.006 0.001 HIS A 103 PHE 0.058 0.003 PHE C 101 TYR 0.027 0.003 TYR B 118 ARG 0.031 0.002 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 307 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASN cc_start: 0.6382 (m-40) cc_final: 0.6012 (t0) REVERT: A 93 THR cc_start: 0.6767 (m) cc_final: 0.6427 (p) REVERT: A 117 GLN cc_start: 0.7812 (mm-40) cc_final: 0.7532 (mm110) REVERT: A 118 LYS cc_start: 0.8075 (mmmt) cc_final: 0.7794 (mmmt) REVERT: A 120 PRO cc_start: 0.5406 (Cg_exo) cc_final: 0.5102 (Cg_endo) REVERT: A 136 GLN cc_start: 0.6005 (mp-120) cc_final: 0.5699 (mp-120) REVERT: A 207 ASP cc_start: 0.6237 (t0) cc_final: 0.5805 (t70) REVERT: A 210 GLU cc_start: 0.7127 (tt0) cc_final: 0.6655 (tt0) REVERT: A 240 LYS cc_start: 0.8117 (mtmm) cc_final: 0.7773 (mtmm) REVERT: A 252 ASN cc_start: 0.5793 (m-40) cc_final: 0.5341 (m-40) REVERT: A 319 GLU cc_start: 0.6261 (tp30) cc_final: 0.5506 (mp0) REVERT: A 340 MET cc_start: 0.5808 (mpp) cc_final: 0.5347 (mpp) REVERT: A 344 PHE cc_start: 0.6396 (p90) cc_final: 0.5666 (p90) REVERT: B 170 TYR cc_start: 0.6288 (t80) cc_final: 0.5781 (t80) REVERT: B 191 LYS cc_start: 0.7925 (ttmt) cc_final: 0.7669 (ttmt) REVERT: B 219 MET cc_start: 0.6929 (mtp) cc_final: 0.6670 (mtp) REVERT: C 120 MET cc_start: 0.7243 (tmm) cc_final: 0.7009 (tmm) REVERT: C 126 LEU cc_start: 0.7175 (mm) cc_final: 0.6932 (mm) REVERT: C 238 LEU cc_start: 0.5780 (mm) cc_final: 0.5528 (mm) REVERT: D 107 PHE cc_start: 0.7502 (t80) cc_final: 0.7094 (t80) REVERT: D 172 ASP cc_start: 0.5930 (t70) cc_final: 0.5548 (t0) REVERT: D 205 THR cc_start: 0.7261 (m) cc_final: 0.7049 (m) REVERT: D 207 ASP cc_start: 0.7391 (t0) cc_final: 0.6866 (t70) REVERT: D 214 MET cc_start: 0.6098 (mtt) cc_final: 0.5501 (mtt) REVERT: D 238 GLU cc_start: 0.7278 (mt-10) cc_final: 0.6819 (mp0) REVERT: D 241 ASN cc_start: 0.6993 (p0) cc_final: 0.6653 (p0) REVERT: D 250 GLU cc_start: 0.6292 (mp0) cc_final: 0.6065 (mt-10) REVERT: D 253 MET cc_start: 0.7057 (tpt) cc_final: 0.6776 (tpp) REVERT: D 294 LEU cc_start: 0.7889 (mt) cc_final: 0.7628 (mt) REVERT: D 319 GLU cc_start: 0.6526 (tm-30) cc_final: 0.6301 (tm-30) REVERT: D 330 VAL cc_start: 0.5718 (p) cc_final: 0.5409 (p) REVERT: D 360 MET cc_start: 0.3275 (mmp) cc_final: 0.2967 (mmp) outliers start: 11 outliers final: 4 residues processed: 317 average time/residue: 0.2235 time to fit residues: 98.0000 Evaluate side-chains 283 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 279 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 366 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 42 ASN C 28 ASN D 252 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.179011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.150997 restraints weight = 14383.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.155574 restraints weight = 7476.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.158729 restraints weight = 4736.916| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10041 Z= 0.246 Angle : 0.724 10.207 13616 Z= 0.370 Chirality : 0.047 0.194 1597 Planarity : 0.005 0.053 1723 Dihedral : 5.422 63.721 1347 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.15 % Allowed : 12.53 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.24), residues: 1232 helix: 0.99 (0.22), residues: 601 sheet: 0.39 (0.38), residues: 209 loop : -1.77 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 110 HIS 0.004 0.001 HIS A 146 PHE 0.022 0.002 PHE C 138 TYR 0.018 0.001 TYR C 148 ARG 0.006 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 281 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 THR cc_start: 0.6894 (m) cc_final: 0.6643 (p) REVERT: A 120 PRO cc_start: 0.6602 (Cg_exo) cc_final: 0.6388 (Cg_endo) REVERT: A 136 GLN cc_start: 0.6576 (mp-120) cc_final: 0.6256 (mp-120) REVERT: A 143 ARG cc_start: 0.8107 (tpp-160) cc_final: 0.7840 (tpp80) REVERT: A 187 GLN cc_start: 0.7270 (mm-40) cc_final: 0.6987 (mm-40) REVERT: A 252 ASN cc_start: 0.7238 (m-40) cc_final: 0.6635 (m-40) REVERT: A 253 MET cc_start: 0.7478 (tpp) cc_final: 0.7245 (tpt) REVERT: A 294 LEU cc_start: 0.8541 (tp) cc_final: 0.8218 (mm) REVERT: A 317 VAL cc_start: 0.8592 (t) cc_final: 0.8368 (p) REVERT: A 320 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.6810 (mtm180) REVERT: A 344 PHE cc_start: 0.6593 (p90) cc_final: 0.6241 (p90) REVERT: B 102 LEU cc_start: 0.7358 (tp) cc_final: 0.7147 (tt) REVERT: B 170 TYR cc_start: 0.7231 (t80) cc_final: 0.6587 (t80) REVERT: B 191 LYS cc_start: 0.7709 (ttmt) cc_final: 0.7484 (ttmt) REVERT: C 26 ILE cc_start: 0.8456 (tt) cc_final: 0.8218 (tp) REVERT: C 111 MET cc_start: 0.5911 (OUTLIER) cc_final: 0.5478 (ttm) REVERT: C 242 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6928 (mm) REVERT: D 107 PHE cc_start: 0.7360 (t80) cc_final: 0.7125 (t80) REVERT: D 172 ASP cc_start: 0.6160 (t70) cc_final: 0.5826 (t0) REVERT: D 187 GLN cc_start: 0.7258 (mm-40) cc_final: 0.6776 (mm-40) REVERT: D 210 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6886 (mm-30) REVERT: D 222 ARG cc_start: 0.7656 (ttt180) cc_final: 0.7197 (ttp-170) REVERT: D 327 LEU cc_start: 0.7597 (tt) cc_final: 0.7385 (tp) REVERT: D 328 GLU cc_start: 0.6955 (pp20) cc_final: 0.6602 (pp20) outliers start: 45 outliers final: 25 residues processed: 301 average time/residue: 0.2308 time to fit residues: 95.9135 Evaluate side-chains 290 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 262 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 351 ASP Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 366 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 16 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 42 ASN A 88 ASN A 354 HIS D 42 ASN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN D 354 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.178075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.149792 restraints weight = 14570.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.154371 restraints weight = 7534.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.157234 restraints weight = 4769.290| |-----------------------------------------------------------------------------| r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10041 Z= 0.220 Angle : 0.654 8.544 13616 Z= 0.332 Chirality : 0.045 0.149 1597 Planarity : 0.005 0.049 1723 Dihedral : 4.839 55.352 1343 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.15 % Allowed : 16.22 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.25), residues: 1232 helix: 1.09 (0.22), residues: 596 sheet: 0.47 (0.39), residues: 209 loop : -1.72 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 136 HIS 0.008 0.001 HIS A 146 PHE 0.031 0.002 PHE D 243 TYR 0.017 0.001 TYR D 236 ARG 0.005 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 274 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 PRO cc_start: 0.6634 (Cg_exo) cc_final: 0.6403 (Cg_endo) REVERT: A 136 GLN cc_start: 0.6553 (mp-120) cc_final: 0.6228 (mp-120) REVERT: A 143 ARG cc_start: 0.8160 (tpp-160) cc_final: 0.7935 (tpp80) REVERT: A 187 GLN cc_start: 0.7203 (mm-40) cc_final: 0.6914 (tp-100) REVERT: A 240 LYS cc_start: 0.8210 (mtmm) cc_final: 0.7958 (mtmm) REVERT: A 317 VAL cc_start: 0.8593 (t) cc_final: 0.8366 (p) REVERT: A 320 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6814 (mtm180) REVERT: A 344 PHE cc_start: 0.6550 (p90) cc_final: 0.6068 (p90) REVERT: B 102 LEU cc_start: 0.7358 (tp) cc_final: 0.7150 (tt) REVERT: B 147 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7006 (mpp) REVERT: B 191 LYS cc_start: 0.7772 (ttmt) cc_final: 0.7551 (ttmt) REVERT: B 215 MET cc_start: 0.5575 (tmm) cc_final: 0.5258 (tmm) REVERT: C 26 ILE cc_start: 0.8399 (tt) cc_final: 0.8140 (tp) REVERT: C 49 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7937 (tt) REVERT: C 85 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7634 (tp) REVERT: D 107 PHE cc_start: 0.7344 (t80) cc_final: 0.7132 (t80) REVERT: D 172 ASP cc_start: 0.6056 (t70) cc_final: 0.5699 (t70) REVERT: D 187 GLN cc_start: 0.7127 (mm-40) cc_final: 0.6774 (mm-40) REVERT: D 214 MET cc_start: 0.6156 (mtt) cc_final: 0.5559 (mtt) REVERT: D 217 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6742 (mtp-110) REVERT: D 327 LEU cc_start: 0.7569 (tt) cc_final: 0.7335 (tp) REVERT: D 333 LEU cc_start: 0.7369 (mt) cc_final: 0.7154 (mt) outliers start: 45 outliers final: 26 residues processed: 297 average time/residue: 0.2293 time to fit residues: 94.2803 Evaluate side-chains 294 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 263 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 79 CYS Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 366 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 121 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 112 optimal weight: 7.9990 chunk 33 optimal weight: 0.0970 chunk 92 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN B 27 ASN D 42 ASN D 146 HIS D 154 GLN D 185 GLN D 335 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.179023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.151345 restraints weight = 14272.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.155667 restraints weight = 7557.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.158813 restraints weight = 4884.744| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10041 Z= 0.186 Angle : 0.626 9.560 13616 Z= 0.316 Chirality : 0.044 0.181 1597 Planarity : 0.005 0.049 1723 Dihedral : 4.576 46.419 1341 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.06 % Allowed : 19.08 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1232 helix: 1.16 (0.22), residues: 593 sheet: 0.62 (0.39), residues: 209 loop : -1.54 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 136 HIS 0.009 0.001 HIS A 146 PHE 0.019 0.001 PHE D 243 TYR 0.020 0.001 TYR D 236 ARG 0.004 0.000 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 267 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 PRO cc_start: 0.6604 (Cg_exo) cc_final: 0.6370 (Cg_endo) REVERT: A 136 GLN cc_start: 0.6533 (mp-120) cc_final: 0.6195 (mp-120) REVERT: A 294 LEU cc_start: 0.8437 (tp) cc_final: 0.8056 (mm) REVERT: A 317 VAL cc_start: 0.8547 (t) cc_final: 0.8241 (p) REVERT: A 320 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.6825 (mtm180) REVERT: A 344 PHE cc_start: 0.6501 (p90) cc_final: 0.6007 (p90) REVERT: B 102 LEU cc_start: 0.7440 (tp) cc_final: 0.7213 (tt) REVERT: B 147 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.6996 (mpp) REVERT: B 191 LYS cc_start: 0.7683 (ttmt) cc_final: 0.7476 (ttmt) REVERT: B 215 MET cc_start: 0.5587 (tmm) cc_final: 0.5381 (tmm) REVERT: C 26 ILE cc_start: 0.8365 (tt) cc_final: 0.8131 (tp) REVERT: C 49 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7764 (tt) REVERT: C 206 VAL cc_start: 0.8040 (OUTLIER) cc_final: 0.7807 (p) REVERT: D 172 ASP cc_start: 0.6081 (t70) cc_final: 0.5759 (t70) REVERT: D 187 GLN cc_start: 0.6803 (OUTLIER) cc_final: 0.5525 (tt0) REVERT: D 323 LYS cc_start: 0.7694 (mtmm) cc_final: 0.7493 (mtmt) outliers start: 44 outliers final: 27 residues processed: 291 average time/residue: 0.2290 time to fit residues: 92.0686 Evaluate side-chains 291 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 259 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain D residue 366 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 42 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 116 optimal weight: 30.0000 chunk 38 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.176454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.147767 restraints weight = 14540.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.152457 restraints weight = 7570.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.155584 restraints weight = 4786.489| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10041 Z= 0.258 Angle : 0.645 10.089 13616 Z= 0.329 Chirality : 0.045 0.140 1597 Planarity : 0.005 0.047 1723 Dihedral : 4.608 38.774 1341 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.98 % Allowed : 20.46 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1232 helix: 1.06 (0.22), residues: 592 sheet: 0.74 (0.40), residues: 202 loop : -1.47 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 368 HIS 0.009 0.001 HIS A 146 PHE 0.022 0.002 PHE D 203 TYR 0.010 0.001 TYR B 223 ARG 0.002 0.000 ARG D 320 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 263 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 PRO cc_start: 0.6739 (Cg_exo) cc_final: 0.6530 (Cg_endo) REVERT: A 136 GLN cc_start: 0.6606 (mp-120) cc_final: 0.6258 (mp-120) REVERT: A 213 THR cc_start: 0.7994 (m) cc_final: 0.7774 (m) REVERT: A 317 VAL cc_start: 0.8491 (t) cc_final: 0.8241 (p) REVERT: A 320 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6786 (mtm180) REVERT: A 338 MET cc_start: 0.7248 (mmp) cc_final: 0.6984 (mmt) REVERT: A 344 PHE cc_start: 0.6521 (p90) cc_final: 0.6041 (p90) REVERT: B 102 LEU cc_start: 0.7525 (tp) cc_final: 0.7293 (tt) REVERT: B 147 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7308 (mtt) REVERT: C 105 MET cc_start: 0.6265 (mtt) cc_final: 0.6015 (mtm) REVERT: C 111 MET cc_start: 0.6073 (OUTLIER) cc_final: 0.5630 (ttm) REVERT: C 206 VAL cc_start: 0.8059 (OUTLIER) cc_final: 0.7805 (p) REVERT: D 36 LEU cc_start: 0.8543 (tt) cc_final: 0.8318 (tp) REVERT: D 214 MET cc_start: 0.5957 (OUTLIER) cc_final: 0.5333 (tpp) REVERT: D 295 ARG cc_start: 0.7713 (mmt180) cc_final: 0.7069 (mmt180) REVERT: D 319 GLU cc_start: 0.6544 (tm-30) cc_final: 0.6138 (tm-30) outliers start: 54 outliers final: 37 residues processed: 288 average time/residue: 0.2333 time to fit residues: 92.7125 Evaluate side-chains 303 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 261 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 117 GLN Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 340 MET Chi-restraints excluded: chain D residue 366 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 58 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.176157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.147548 restraints weight = 14591.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.152203 restraints weight = 7662.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.155406 restraints weight = 4869.591| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10041 Z= 0.219 Angle : 0.626 9.482 13616 Z= 0.318 Chirality : 0.044 0.133 1597 Planarity : 0.004 0.046 1723 Dihedral : 4.515 37.617 1341 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 5.25 % Allowed : 21.29 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1232 helix: 1.03 (0.22), residues: 596 sheet: 0.59 (0.40), residues: 202 loop : -1.38 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 368 HIS 0.009 0.001 HIS A 146 PHE 0.021 0.002 PHE D 203 TYR 0.033 0.001 TYR A 322 ARG 0.003 0.000 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 272 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 GLN cc_start: 0.6649 (mp-120) cc_final: 0.6265 (mp-120) REVERT: A 213 THR cc_start: 0.8044 (m) cc_final: 0.7819 (m) REVERT: A 317 VAL cc_start: 0.8454 (t) cc_final: 0.8208 (p) REVERT: A 320 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.6643 (mtm180) REVERT: A 344 PHE cc_start: 0.6527 (p90) cc_final: 0.6066 (p90) REVERT: B 102 LEU cc_start: 0.7546 (tp) cc_final: 0.7343 (tt) REVERT: B 147 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7321 (mtt) REVERT: C 49 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7791 (tt) REVERT: C 111 MET cc_start: 0.5995 (OUTLIER) cc_final: 0.5591 (ttm) REVERT: C 203 SER cc_start: 0.8130 (m) cc_final: 0.7776 (t) REVERT: C 206 VAL cc_start: 0.8055 (OUTLIER) cc_final: 0.7805 (p) REVERT: D 295 ARG cc_start: 0.7693 (mmt180) cc_final: 0.7148 (mmt180) REVERT: D 323 LYS cc_start: 0.8001 (mtmm) cc_final: 0.7631 (mtmt) REVERT: D 328 GLU cc_start: 0.6937 (pt0) cc_final: 0.6533 (pt0) outliers start: 57 outliers final: 40 residues processed: 298 average time/residue: 0.2198 time to fit residues: 90.6405 Evaluate side-chains 309 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 264 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 117 GLN Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 340 MET Chi-restraints excluded: chain D residue 366 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.172647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.143606 restraints weight = 14796.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.148169 restraints weight = 7714.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.151363 restraints weight = 4912.417| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10041 Z= 0.308 Angle : 0.664 8.123 13616 Z= 0.342 Chirality : 0.046 0.157 1597 Planarity : 0.005 0.047 1723 Dihedral : 4.621 38.163 1341 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 5.71 % Allowed : 22.67 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.24), residues: 1232 helix: 0.88 (0.22), residues: 598 sheet: 0.51 (0.39), residues: 204 loop : -1.39 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 136 HIS 0.009 0.001 HIS A 146 PHE 0.027 0.002 PHE D 203 TYR 0.025 0.001 TYR A 322 ARG 0.005 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 271 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 GLN cc_start: 0.6662 (mp-120) cc_final: 0.6258 (mp-120) REVERT: A 344 PHE cc_start: 0.6569 (p90) cc_final: 0.6046 (p90) REVERT: B 27 ASN cc_start: 0.8137 (m110) cc_final: 0.7893 (m-40) REVERT: B 81 VAL cc_start: 0.8228 (OUTLIER) cc_final: 0.7966 (p) REVERT: B 102 LEU cc_start: 0.7673 (tp) cc_final: 0.7462 (tt) REVERT: B 147 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.7443 (mtt) REVERT: B 165 MET cc_start: 0.7780 (tpt) cc_final: 0.6824 (tpt) REVERT: B 170 TYR cc_start: 0.7112 (t80) cc_final: 0.6459 (t80) REVERT: B 217 PRO cc_start: 0.7899 (Cg_exo) cc_final: 0.7663 (Cg_endo) REVERT: C 49 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7881 (tt) REVERT: C 111 MET cc_start: 0.6139 (OUTLIER) cc_final: 0.5733 (ttm) REVERT: C 203 SER cc_start: 0.8210 (m) cc_final: 0.7755 (p) REVERT: D 217 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.7141 (mtp-110) REVERT: D 244 VAL cc_start: 0.7910 (m) cc_final: 0.7561 (p) REVERT: D 323 LYS cc_start: 0.8015 (mtmm) cc_final: 0.7611 (mtmt) outliers start: 62 outliers final: 41 residues processed: 294 average time/residue: 0.2253 time to fit residues: 91.4276 Evaluate side-chains 312 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 266 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 117 GLN Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 340 MET Chi-restraints excluded: chain D residue 366 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 111 optimal weight: 20.0000 chunk 82 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 115 optimal weight: 0.0970 chunk 27 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.176446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.147665 restraints weight = 14714.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.152247 restraints weight = 7658.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.155533 restraints weight = 4839.985| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10041 Z= 0.186 Angle : 0.631 8.947 13616 Z= 0.318 Chirality : 0.044 0.147 1597 Planarity : 0.004 0.048 1723 Dihedral : 4.370 33.587 1341 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.15 % Allowed : 25.16 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.25), residues: 1232 helix: 1.12 (0.22), residues: 597 sheet: 0.38 (0.40), residues: 204 loop : -1.28 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 368 HIS 0.010 0.001 HIS A 146 PHE 0.018 0.001 PHE C 133 TYR 0.027 0.001 TYR A 322 ARG 0.002 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 271 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 GLN cc_start: 0.6674 (mp-120) cc_final: 0.6241 (mp-120) REVERT: A 213 THR cc_start: 0.8038 (m) cc_final: 0.7781 (t) REVERT: A 320 ARG cc_start: 0.6644 (mtm180) cc_final: 0.6354 (mtm180) REVERT: A 344 PHE cc_start: 0.6379 (p90) cc_final: 0.5928 (p90) REVERT: B 102 LEU cc_start: 0.7637 (tp) cc_final: 0.7430 (tt) REVERT: B 147 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.7321 (mtt) REVERT: B 165 MET cc_start: 0.7762 (tpt) cc_final: 0.6549 (tpt) REVERT: C 49 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7844 (tt) REVERT: C 203 SER cc_start: 0.8033 (m) cc_final: 0.7679 (p) REVERT: D 295 ARG cc_start: 0.7596 (mmt180) cc_final: 0.6933 (mmt180) REVERT: D 323 LYS cc_start: 0.8035 (mtmm) cc_final: 0.7618 (mtmt) REVERT: D 369 GLU cc_start: 0.7078 (pm20) cc_final: 0.6781 (pm20) outliers start: 45 outliers final: 33 residues processed: 287 average time/residue: 0.2220 time to fit residues: 87.4866 Evaluate side-chains 301 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 266 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 340 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 27 optimal weight: 9.9990 chunk 119 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 1 optimal weight: 0.0010 chunk 9 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 88 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 164 ASN ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.174450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.145545 restraints weight = 14720.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.150146 restraints weight = 7728.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.153289 restraints weight = 4913.983| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10041 Z= 0.231 Angle : 0.646 9.527 13616 Z= 0.325 Chirality : 0.044 0.143 1597 Planarity : 0.004 0.047 1723 Dihedral : 4.250 35.805 1338 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.96 % Allowed : 25.71 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.25), residues: 1232 helix: 1.07 (0.22), residues: 604 sheet: 0.52 (0.40), residues: 199 loop : -1.31 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 250 HIS 0.009 0.001 HIS A 146 PHE 0.021 0.002 PHE D 203 TYR 0.026 0.001 TYR A 322 ARG 0.002 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 270 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 GLN cc_start: 0.6670 (mp-120) cc_final: 0.6252 (mp-120) REVERT: A 201 PHE cc_start: 0.7518 (m-80) cc_final: 0.7276 (m-10) REVERT: A 320 ARG cc_start: 0.6630 (mtm180) cc_final: 0.6343 (mtm180) REVERT: A 344 PHE cc_start: 0.6405 (p90) cc_final: 0.5954 (p90) REVERT: B 81 VAL cc_start: 0.8204 (OUTLIER) cc_final: 0.7935 (p) REVERT: B 147 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7378 (mtt) REVERT: B 165 MET cc_start: 0.7777 (tpt) cc_final: 0.6975 (tpt) REVERT: B 217 PRO cc_start: 0.7864 (Cg_exo) cc_final: 0.7611 (Cg_endo) REVERT: C 49 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7870 (tt) REVERT: C 133 PHE cc_start: 0.7365 (m-80) cc_final: 0.6980 (t80) REVERT: C 203 SER cc_start: 0.8057 (m) cc_final: 0.7712 (p) REVERT: D 323 LYS cc_start: 0.8061 (mtmm) cc_final: 0.7752 (mtmt) REVERT: D 369 GLU cc_start: 0.7083 (pm20) cc_final: 0.6713 (pm20) outliers start: 43 outliers final: 33 residues processed: 288 average time/residue: 0.2422 time to fit residues: 97.1821 Evaluate side-chains 302 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 266 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 340 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 91 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 10 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.173928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.146516 restraints weight = 14739.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.150804 restraints weight = 7948.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.153777 restraints weight = 5133.308| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10041 Z= 0.193 Angle : 0.660 10.160 13616 Z= 0.328 Chirality : 0.044 0.167 1597 Planarity : 0.004 0.050 1723 Dihedral : 4.194 34.093 1338 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.50 % Allowed : 26.73 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.25), residues: 1232 helix: 1.13 (0.22), residues: 604 sheet: 0.45 (0.40), residues: 201 loop : -1.29 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 368 HIS 0.010 0.001 HIS A 146 PHE 0.020 0.001 PHE C 133 TYR 0.026 0.001 TYR A 322 ARG 0.002 0.000 ARG B 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 267 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 MET cc_start: 0.5378 (tpp) cc_final: 0.4903 (tpp) REVERT: A 136 GLN cc_start: 0.6708 (mp-120) cc_final: 0.6271 (mp-120) REVERT: A 213 THR cc_start: 0.7957 (m) cc_final: 0.7615 (t) REVERT: A 240 LYS cc_start: 0.8526 (mtmm) cc_final: 0.8281 (mtmm) REVERT: A 320 ARG cc_start: 0.6594 (mtm180) cc_final: 0.6300 (mtm180) REVERT: A 344 PHE cc_start: 0.6367 (p90) cc_final: 0.5949 (p90) REVERT: B 81 VAL cc_start: 0.8200 (OUTLIER) cc_final: 0.7913 (p) REVERT: B 147 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.7323 (mtt) REVERT: B 165 MET cc_start: 0.7767 (tpt) cc_final: 0.6569 (tpt) REVERT: B 217 PRO cc_start: 0.7827 (Cg_exo) cc_final: 0.7586 (Cg_endo) REVERT: C 49 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7812 (tt) REVERT: C 133 PHE cc_start: 0.7267 (m-80) cc_final: 0.6920 (t80) REVERT: C 203 SER cc_start: 0.8027 (m) cc_final: 0.7709 (p) REVERT: C 249 GLN cc_start: 0.6933 (tp-100) cc_final: 0.6647 (tp40) REVERT: D 173 GLU cc_start: 0.7442 (tp30) cc_final: 0.7108 (mt-10) REVERT: D 323 LYS cc_start: 0.8013 (mtmm) cc_final: 0.7652 (mtmt) REVERT: D 369 GLU cc_start: 0.7035 (pm20) cc_final: 0.6675 (pm20) outliers start: 38 outliers final: 34 residues processed: 281 average time/residue: 0.2242 time to fit residues: 86.6517 Evaluate side-chains 303 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 266 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 185 GLN Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 340 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 12 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.172873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.145734 restraints weight = 14956.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.149902 restraints weight = 8040.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.152780 restraints weight = 5207.318| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10041 Z= 0.201 Angle : 0.650 10.279 13616 Z= 0.324 Chirality : 0.044 0.155 1597 Planarity : 0.004 0.048 1723 Dihedral : 4.146 34.663 1337 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.50 % Allowed : 26.73 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.25), residues: 1232 helix: 1.13 (0.22), residues: 606 sheet: 0.46 (0.40), residues: 201 loop : -1.26 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 368 HIS 0.010 0.001 HIS A 146 PHE 0.048 0.002 PHE C 101 TYR 0.025 0.001 TYR A 322 ARG 0.002 0.000 ARG A 300 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3197.03 seconds wall clock time: 58 minutes 7.05 seconds (3487.05 seconds total)