Starting phenix.real_space_refine on Thu Jul 2 21:17:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dne_27564/07_2026/8dne_27564.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dne_27564/07_2026/8dne_27564.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/8dne_27564/07_2026/8dne_27564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dne_27564/07_2026/8dne_27564.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8dne_27564/07_2026/8dne_27564.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dne_27564/07_2026/8dne_27564.cif" model { file = "/net/cci-nas-00/data/ceres_data/8dne_27564/07_2026/8dne_27564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dne_27564/07_2026/8dne_27564.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.065 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 28 5.16 5 C 6841 2.51 5 N 1609 2.21 5 O 1795 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10281 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2976 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 11, 'TRANS': 359} Chain breaks: 2 Chain: "B" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2131 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 11, 'TRANS': 243} Chain: "C" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2979 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 11, 'TRANS': 358} Chain breaks: 2 Chain: "D" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2131 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 11, 'TRANS': 243} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.35, per 1000 atoms: 0.23 Number of scatterers: 10281 At special positions: 0 Unit cell: (91.8, 85.32, 136.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 6 15.00 Mg 2 11.99 O 1795 8.00 N 1609 7.00 C 6841 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: 1.02 Conformation dependent library (CDL) restraints added in 358.6 milliseconds 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 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: 43 helices and 10 sheets defined 52.0% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 16 through 26 removed outlier: 3.603A pdb=" N ILE A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N PHE A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 68 Processing helix chain 'A' and resid 99 through 112 Processing helix chain 'A' and resid 114 through 130 removed outlier: 3.557A pdb=" N ILE A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N GLU A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 143 through 157 removed outlier: 3.702A pdb=" N HIS A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 191 removed outlier: 3.597A pdb=" N GLY A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 207 removed outlier: 3.581A pdb=" N VAL A 204 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 240 Processing helix chain 'B' and resid 3 through 18 Processing helix chain 'B' and resid 21 through 47 removed outlier: 3.959A pdb=" N ILE B 25 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TRP B 26 " --> pdb=" O VAL B 22 " (cutoff:3.500A) Proline residue: B 32 - end of helix removed outlier: 4.431A pdb=" N HIS B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 82 Proline residue: B 70 - end of helix Processing helix chain 'B' and resid 83 through 88 removed outlier: 3.658A pdb=" N GLU B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS B 88 " --> pdb=" O ILE B 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 83 through 88' Processing helix chain 'B' and resid 88 through 93 removed outlier: 3.733A pdb=" N THR B 93 " --> pdb=" O LYS B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 126 removed outlier: 3.732A pdb=" N VAL B 121 " --> pdb=" O GLY B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 138 removed outlier: 5.123A pdb=" N TYR B 138 " --> pdb=" O LYS B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 163 removed outlier: 3.872A pdb=" N ALA B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY B 155 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET B 156 " --> pdb=" O PHE B 152 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL B 163 " --> pdb=" O GLY B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 180 removed outlier: 3.948A pdb=" N GLY B 173 " --> pdb=" O LYS B 169 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 201 removed outlier: 3.511A pdb=" N LEU B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 218 Processing helix chain 'B' and resid 223 through 256 Proline residue: B 235 - end of helix removed outlier: 3.579A pdb=" N LEU B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LYS B 250 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ASP B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 256 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 27 removed outlier: 4.105A pdb=" N LEU C 21 " --> pdb=" O PRO C 17 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE C 24 " --> pdb=" O ARG C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 68 Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 114 through 129 removed outlier: 4.974A pdb=" N SER C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLU C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE C 128 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER C 129 " --> pdb=" O ILE C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 137 removed outlier: 4.229A pdb=" N ASN C 136 " --> pdb=" O ASP C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.527A pdb=" N TYR C 142 " --> pdb=" O LEU C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 157 Processing helix chain 'C' and resid 173 through 190 removed outlier: 3.528A pdb=" N LYS C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 208 removed outlier: 4.010A pdb=" N VAL C 204 " --> pdb=" O ASP C 200 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS C 205 " --> pdb=" O MET C 201 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE C 206 " --> pdb=" O ASN C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 239 Processing helix chain 'D' and resid 3 through 17 Processing helix chain 'D' and resid 26 through 44 Proline residue: D 32 - end of helix Processing helix chain 'D' and resid 55 through 82 Proline residue: D 70 - end of helix removed outlier: 3.613A pdb=" N THR D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 93 removed outlier: 3.616A pdb=" N PHE D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 88 through 93' Processing helix chain 'D' and resid 100 through 129 removed outlier: 3.628A pdb=" N VAL D 106 " --> pdb=" O PHE D 102 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ASN D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY D 117 " --> pdb=" O ASN D 113 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR D 128 " --> pdb=" O ILE D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 138 removed outlier: 4.900A pdb=" N TYR D 138 " --> pdb=" O LYS D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 165 removed outlier: 3.963A pdb=" N SER D 151 " --> pdb=" O MET D 147 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR D 160 " --> pdb=" O MET D 156 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL D 163 " --> pdb=" O GLY D 159 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE D 164 " --> pdb=" O THR D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 180 Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.962A pdb=" N LEU D 199 " --> pdb=" O PHE D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 217 removed outlier: 4.362A pdb=" N VAL D 208 " --> pdb=" O PRO D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 233 Processing helix chain 'D' and resid 233 through 256 removed outlier: 3.520A pdb=" N LEU D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LYS D 250 " --> pdb=" O LYS D 246 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ASP D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 43 removed outlier: 7.110A pdb=" N LEU A 34 " --> pdb=" O LYS A 12 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LYS A 12 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL A 36 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LYS A 10 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LYS A 38 " --> pdb=" O TRP A 8 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N TRP A 8 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ILE A 40 " --> pdb=" O ASP A 6 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL A 7 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS A 75 " --> pdb=" O VAL A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 87 removed outlier: 6.588A pdb=" N VAL A 85 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ASP A 166 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU A 87 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE A 163 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N VAL A 197 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE A 165 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU A 50 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY A 51 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU A 214 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL A 53 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA A 211 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU A 222 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU A 213 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 257 through 265 removed outlier: 5.200A pdb=" N ILE A 259 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N GLU A 287 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 288 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN C 390 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU C 388 " --> pdb=" O LYS A 333 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 273 through 276 removed outlier: 5.999A pdb=" N PHE A 274 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY A 373 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N HIS A 350 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL A 296 " --> pdb=" O HIS A 350 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 310 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASP A 303 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASP A 308 " --> pdb=" O ASP A 303 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AA6, first strand: chain 'A' and resid 388 through 394 removed outlier: 3.549A pdb=" N LYS C 333 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN A 390 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR C 331 " --> pdb=" O ASN A 390 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG A 392 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 394 " --> pdb=" O LYS C 327 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LYS C 327 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU C 261 " --> pdb=" O ASP C 285 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLU C 287 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE C 259 " --> pdb=" O GLU C 287 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 44 removed outlier: 3.569A pdb=" N GLU C 32 " --> pdb=" O TYR C 13 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYS C 9 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LYS C 38 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL C 7 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE C 40 " --> pdb=" O PHE C 5 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N PHE C 5 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU C 42 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ARG C 3 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL C 7 " --> pdb=" O LYS C 75 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LYS C 75 " --> pdb=" O VAL C 7 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 84 through 87 removed outlier: 4.346A pdb=" N ASP C 166 " --> pdb=" O LEU C 87 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N PHE C 163 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL C 197 " --> pdb=" O PHE C 163 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE C 165 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL C 49 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILE C 212 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLY C 51 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU C 214 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL C 53 " --> pdb=" O LEU C 214 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU C 221 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 276 removed outlier: 6.619A pdb=" N PHE C 274 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLY C 373 " --> pdb=" O PHE C 274 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 308 through 313 removed outlier: 6.714A pdb=" N ILE C 301 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY C 311 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE C 299 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASN C 313 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA C 297 " --> pdb=" O ASN C 313 " (cutoff:3.500A) 498 hydrogen bonds defined for protein. 1443 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.53 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3019 1.34 - 1.46: 1762 1.46 - 1.57: 5707 1.57 - 1.69: 10 1.69 - 1.81: 46 Bond restraints: 10544 Sorted by residual: bond pdb=" N ILE C 135 " pdb=" CA ILE C 135 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.28e+00 bond pdb=" N VAL D 186 " pdb=" CA VAL D 186 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.41e-02 5.03e+03 6.38e+00 bond pdb=" N VAL B 186 " pdb=" CA VAL B 186 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.25e-02 6.40e+03 5.51e+00 bond pdb=" N TYR D 187 " pdb=" CA TYR D 187 " ideal model delta sigma weight residual 1.455 1.483 -0.028 1.21e-02 6.83e+03 5.30e+00 bond pdb=" O5' ATP C 502 " pdb=" PA ATP C 502 " ideal model delta sigma weight residual 1.579 1.602 -0.023 1.10e-02 8.26e+03 4.52e+00 ... (remaining 10539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 13977 1.91 - 3.82: 238 3.82 - 5.73: 45 5.73 - 7.64: 3 7.64 - 9.55: 6 Bond angle restraints: 14269 Sorted by residual: angle pdb=" PA ATP A 502 " pdb=" O3A ATP A 502 " pdb=" PB ATP A 502 " ideal model delta sigma weight residual 136.83 127.51 9.32 1.00e+00 1.00e+00 8.69e+01 angle pdb=" PB ATP A 502 " pdb=" O3B ATP A 502 " pdb=" PG ATP A 502 " ideal model delta sigma weight residual 139.87 131.01 8.86 1.00e+00 1.00e+00 7.85e+01 angle pdb=" PB ATP C 502 " pdb=" O3B ATP C 502 " pdb=" PG ATP C 502 " ideal model delta sigma weight residual 139.87 131.87 8.00 1.00e+00 1.00e+00 6.39e+01 angle pdb=" N ILE D 47 " pdb=" CA ILE D 47 " pdb=" C ILE D 47 " ideal model delta sigma weight residual 113.71 109.05 4.66 9.50e-01 1.11e+00 2.40e+01 angle pdb=" C5' ATP A 502 " pdb=" O5' ATP A 502 " pdb=" PA ATP A 502 " ideal model delta sigma weight residual 121.27 116.98 4.29 1.00e+00 1.00e+00 1.84e+01 ... (remaining 14264 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5512 17.98 - 35.95: 528 35.95 - 53.93: 84 53.93 - 71.90: 12 71.90 - 89.88: 9 Dihedral angle restraints: 6145 sinusoidal: 2506 harmonic: 3639 Sorted by residual: dihedral pdb=" CA ARG A 27 " pdb=" C ARG A 27 " pdb=" N LYS A 28 " pdb=" CA LYS A 28 " ideal model delta harmonic sigma weight residual 180.00 -154.12 -25.88 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA ASN C 95 " pdb=" C ASN C 95 " pdb=" N TYR C 96 " pdb=" CA TYR C 96 " ideal model delta harmonic sigma weight residual 180.00 -161.76 -18.24 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ASP C 200 " pdb=" C ASP C 200 " pdb=" N MET C 201 " pdb=" CA MET C 201 " ideal model delta harmonic sigma weight residual 180.00 -162.55 -17.45 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 6142 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1461 0.074 - 0.147: 139 0.147 - 0.221: 3 0.221 - 0.294: 0 0.294 - 0.368: 2 Chirality restraints: 1605 Sorted by residual: chirality pdb=" CA VAL D 186 " pdb=" N VAL D 186 " pdb=" C VAL D 186 " pdb=" CB VAL D 186 " both_signs ideal model delta sigma weight residual False 2.44 2.81 -0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CA VAL B 186 " pdb=" N VAL B 186 " pdb=" C VAL B 186 " pdb=" CB VAL B 186 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB ILE C 135 " pdb=" CA ILE C 135 " pdb=" CG1 ILE C 135 " pdb=" CG2 ILE C 135 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.63e-01 ... (remaining 1602 not shown) Planarity restraints: 1737 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 31 " -0.020 2.00e-02 2.50e+03 1.97e-02 9.71e+00 pdb=" CG TRP D 31 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP D 31 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP D 31 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 31 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 31 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 31 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 31 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 31 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP D 31 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 193 " -0.041 5.00e-02 4.00e+02 6.27e-02 6.28e+00 pdb=" N PRO D 194 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 194 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 194 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 31 " 0.041 5.00e-02 4.00e+02 6.21e-02 6.17e+00 pdb=" N PRO B 32 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " 0.035 5.00e-02 4.00e+02 ... (remaining 1734 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 28 2.41 - 3.03: 6180 3.03 - 3.65: 15115 3.65 - 4.28: 21782 4.28 - 4.90: 37041 Nonbonded interactions: 80146 Sorted by model distance: nonbonded pdb="MG MG C 501 " pdb=" O1G ATP C 502 " model vdw 1.785 2.170 nonbonded pdb="MG MG A 501 " pdb=" O1G ATP A 502 " model vdw 1.995 2.170 nonbonded pdb="MG MG A 501 " pdb=" O1B ATP A 502 " model vdw 2.020 2.170 nonbonded pdb=" O SER D 119 " pdb=" OG1 THR D 122 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR D 206 " pdb=" O ASP D 221 " model vdw 2.219 3.040 ... (remaining 80141 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 1 through 240 or resid 254 through 350 or resid 363 throug \ h 393 or resid 501 through 502)) selection = (chain 'C' and (resid 1 through 350 or resid 363 through 502)) } ncs_group { reference = chain 'B' 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.130 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10544 Z= 0.174 Angle : 0.654 9.547 14269 Z= 0.382 Chirality : 0.044 0.368 1605 Planarity : 0.004 0.063 1737 Dihedral : 14.309 89.879 3813 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.24), residues: 1235 helix: 0.40 (0.22), residues: 574 sheet: 0.67 (0.37), residues: 198 loop : -1.42 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 263 TYR 0.021 0.001 TYR B 150 PHE 0.018 0.001 PHE C 30 TRP 0.052 0.002 TRP D 31 HIS 0.004 0.001 HIS D 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (10544) covalent geometry : angle 0.65364 / 0.38 (14269) hydrogen bonds : bond 0.19205 / 12.44 ( 498) hydrogen bonds : angle 7.55797 / 5.28 ( 1443) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.383 Fit side-chains REVERT: B 187 TYR cc_start: 0.8141 (p90) cc_final: 0.7820 (p90) REVERT: C 317 MET cc_start: 0.7857 (mtp) cc_final: 0.7650 (mtp) REVERT: C 362 TRP cc_start: 0.7203 (t60) cc_final: 0.6448 (m-90) REVERT: D 87 GLU cc_start: 0.7018 (tm-30) cc_final: 0.6585 (tm-30) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.0773 time to fit residues: 20.4140 Evaluate side-chains 138 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.0980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 53 HIS C 56 ASN C 230 GLN ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.166088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.132601 restraints weight = 15801.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.135129 restraints weight = 10221.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.137778 restraints weight = 7253.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.138234 restraints weight = 6217.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.138419 restraints weight = 5597.241| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10544 Z= 0.154 Angle : 0.584 8.008 14269 Z= 0.308 Chirality : 0.043 0.177 1605 Planarity : 0.004 0.050 1737 Dihedral : 6.178 80.836 1349 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.27 % Allowed : 10.89 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.24), residues: 1235 helix: 1.11 (0.22), residues: 586 sheet: 0.65 (0.37), residues: 199 loop : -1.58 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 11 TYR 0.019 0.001 TYR B 150 PHE 0.031 0.001 PHE D 72 TRP 0.029 0.002 TRP D 31 HIS 0.006 0.001 HIS B 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (10544) covalent geometry : angle 0.58445 / 0.31 (14269) hydrogen bonds : bond 0.05382 / 3.62 ( 498) hydrogen bonds : angle 5.12341 / 3.55 ( 1443) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 155 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 263 ARG cc_start: 0.5328 (ptt-90) cc_final: 0.4981 (ptp90) REVERT: B 80 ARG cc_start: 0.7936 (ttp-170) cc_final: 0.7508 (ttm170) REVERT: B 110 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7386 (mm-30) REVERT: B 178 ILE cc_start: 0.8501 (pt) cc_final: 0.8265 (mt) REVERT: B 187 TYR cc_start: 0.8583 (p90) cc_final: 0.8072 (p90) REVERT: C 236 MET cc_start: 0.7993 (mmt) cc_final: 0.7750 (mmm) REVERT: C 362 TRP cc_start: 0.7216 (t60) cc_final: 0.6402 (m-90) REVERT: D 8 GLU cc_start: 0.7822 (tp30) cc_final: 0.6959 (tp30) REVERT: D 87 GLU cc_start: 0.7313 (tm-30) cc_final: 0.6947 (tm-30) outliers start: 3 outliers final: 2 residues processed: 157 average time/residue: 0.0809 time to fit residues: 18.9766 Evaluate side-chains 136 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain C residue 228 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 84 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 69 optimal weight: 0.0020 chunk 48 optimal weight: 2.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.163492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.126208 restraints weight = 15658.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.130572 restraints weight = 9304.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.133603 restraints weight = 6651.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.135654 restraints weight = 5283.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.137064 restraints weight = 4505.861| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10544 Z= 0.143 Angle : 0.558 9.408 14269 Z= 0.290 Chirality : 0.042 0.168 1605 Planarity : 0.004 0.045 1737 Dihedral : 6.107 82.909 1349 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.43 % Allowed : 13.39 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.24), residues: 1235 helix: 1.31 (0.22), residues: 587 sheet: 0.63 (0.37), residues: 199 loop : -1.52 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 11 TYR 0.019 0.001 TYR B 150 PHE 0.030 0.001 PHE D 72 TRP 0.030 0.002 TRP D 31 HIS 0.005 0.001 HIS B 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (10544) covalent geometry : angle 0.55829 / 0.29 (14269) hydrogen bonds : bond 0.04835 / 3.26 ( 498) hydrogen bonds : angle 4.75704 / 3.30 ( 1443) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 ARG cc_start: 0.5281 (ptt-90) cc_final: 0.4929 (ptp90) REVERT: B 80 ARG cc_start: 0.8029 (ttp-170) cc_final: 0.7742 (ttp-170) REVERT: B 178 ILE cc_start: 0.8393 (pt) cc_final: 0.8178 (mt) REVERT: B 187 TYR cc_start: 0.8591 (p90) cc_final: 0.8073 (p90) REVERT: D 8 GLU cc_start: 0.7868 (tp30) cc_final: 0.7134 (tp30) REVERT: D 11 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7712 (ttm-80) REVERT: D 80 ARG cc_start: 0.8514 (ttp80) cc_final: 0.8144 (ttm170) REVERT: D 87 GLU cc_start: 0.7439 (tm-30) cc_final: 0.7169 (tm-30) REVERT: D 110 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8243 (mm-30) REVERT: D 175 PHE cc_start: 0.8300 (t80) cc_final: 0.8027 (t80) REVERT: D 179 PHE cc_start: 0.8695 (t80) cc_final: 0.8368 (t80) outliers start: 16 outliers final: 9 residues processed: 159 average time/residue: 0.0781 time to fit residues: 18.5948 Evaluate side-chains 148 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 163 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 47 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 69 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 0.0670 chunk 71 optimal weight: 8.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.167266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.132869 restraints weight = 15871.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.137090 restraints weight = 9448.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.139920 restraints weight = 6734.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.141817 restraints weight = 5358.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.143083 restraints weight = 4580.583| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10544 Z= 0.118 Angle : 0.529 7.965 14269 Z= 0.275 Chirality : 0.042 0.162 1605 Planarity : 0.004 0.041 1737 Dihedral : 5.953 82.911 1349 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.05 % Allowed : 15.00 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.24), residues: 1235 helix: 1.41 (0.22), residues: 589 sheet: 0.77 (0.36), residues: 199 loop : -1.40 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 11 TYR 0.015 0.001 TYR C 391 PHE 0.029 0.001 PHE D 72 TRP 0.034 0.002 TRP D 31 HIS 0.007 0.001 HIS B 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (10544) covalent geometry : angle 0.52869 / 0.28 (14269) hydrogen bonds : bond 0.04325 / 2.92 ( 498) hydrogen bonds : angle 4.53100 / 3.14 ( 1443) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 TYR cc_start: 0.5191 (OUTLIER) cc_final: 0.4644 (t80) REVERT: B 187 TYR cc_start: 0.8536 (p90) cc_final: 0.8050 (p90) REVERT: C 236 MET cc_start: 0.7839 (mmt) cc_final: 0.7610 (mmm) REVERT: C 362 TRP cc_start: 0.7187 (t60) cc_final: 0.6308 (m100) REVERT: D 8 GLU cc_start: 0.7745 (tp30) cc_final: 0.7008 (tp30) REVERT: D 80 ARG cc_start: 0.8458 (ttp80) cc_final: 0.8069 (ttm170) REVERT: D 110 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8135 (mm-30) REVERT: D 179 PHE cc_start: 0.8560 (t80) cc_final: 0.8218 (t80) outliers start: 23 outliers final: 15 residues processed: 162 average time/residue: 0.0822 time to fit residues: 19.9726 Evaluate side-chains 150 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 183 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 121 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.157256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.120519 restraints weight = 16049.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.124771 restraints weight = 9394.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.127699 restraints weight = 6655.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.129628 restraints weight = 5294.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.130976 restraints weight = 4521.708| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 10544 Z= 0.270 Angle : 0.674 7.640 14269 Z= 0.351 Chirality : 0.047 0.205 1605 Planarity : 0.004 0.049 1737 Dihedral : 6.561 86.996 1349 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.86 % Allowed : 17.05 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.24), residues: 1235 helix: 1.00 (0.22), residues: 587 sheet: 0.55 (0.37), residues: 200 loop : -1.56 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 263 TYR 0.029 0.002 TYR B 150 PHE 0.037 0.002 PHE D 72 TRP 0.039 0.003 TRP D 31 HIS 0.005 0.002 HIS B 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00652 / 0.27 (10544) covalent geometry : angle 0.67417 / 0.35 (14269) hydrogen bonds : bond 0.05849 / 3.88 ( 498) hydrogen bonds : angle 4.83871 / 3.35 ( 1443) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 165 ILE cc_start: 0.8215 (tt) cc_final: 0.7777 (pt) REVERT: A 375 LYS cc_start: 0.8489 (tmmt) cc_final: 0.8147 (ttpp) REVERT: B 80 ARG cc_start: 0.8042 (ttp-170) cc_final: 0.7719 (ttp-170) REVERT: B 166 ARG cc_start: 0.8342 (mmt180) cc_final: 0.7958 (mmt180) REVERT: B 187 TYR cc_start: 0.8789 (p90) cc_final: 0.7965 (p90) REVERT: C 148 MET cc_start: 0.7020 (OUTLIER) cc_final: 0.6802 (tmm) REVERT: C 362 TRP cc_start: 0.7377 (t60) cc_final: 0.6257 (m-90) REVERT: D 8 GLU cc_start: 0.8015 (tp30) cc_final: 0.6981 (tp30) REVERT: D 12 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.7365 (mt0) REVERT: D 31 TRP cc_start: 0.6450 (t-100) cc_final: 0.6189 (t-100) REVERT: D 37 LEU cc_start: 0.7684 (mt) cc_final: 0.7456 (mm) REVERT: D 47 ILE cc_start: 0.5497 (OUTLIER) cc_final: 0.5182 (mp) REVERT: D 179 PHE cc_start: 0.8603 (t80) cc_final: 0.8209 (t80) outliers start: 32 outliers final: 17 residues processed: 169 average time/residue: 0.0825 time to fit residues: 20.6876 Evaluate side-chains 161 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 228 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 43 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 118 optimal weight: 0.0060 chunk 98 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 93 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.162269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.125796 restraints weight = 16023.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.130400 restraints weight = 9090.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.133472 restraints weight = 6314.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.135520 restraints weight = 4960.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.136931 restraints weight = 4216.599| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10544 Z= 0.124 Angle : 0.553 8.057 14269 Z= 0.289 Chirality : 0.042 0.188 1605 Planarity : 0.004 0.044 1737 Dihedral : 6.224 87.935 1349 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.41 % Allowed : 18.93 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.24), residues: 1235 helix: 1.32 (0.22), residues: 592 sheet: 0.71 (0.35), residues: 207 loop : -1.48 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 11 TYR 0.017 0.001 TYR B 63 PHE 0.029 0.001 PHE D 255 TRP 0.035 0.002 TRP D 31 HIS 0.014 0.001 HIS B 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (10544) covalent geometry : angle 0.55270 / 0.29 (14269) hydrogen bonds : bond 0.04373 / 2.95 ( 498) hydrogen bonds : angle 4.50878 / 3.11 ( 1443) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 139 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7628 (tp) REVERT: A 375 LYS cc_start: 0.8473 (tmmt) cc_final: 0.8131 (ttpp) REVERT: B 89 LYS cc_start: 0.8832 (ttmt) cc_final: 0.8331 (ttpp) REVERT: B 187 TYR cc_start: 0.8533 (p90) cc_final: 0.7838 (p90) REVERT: C 236 MET cc_start: 0.7925 (mmt) cc_final: 0.7682 (mmm) REVERT: C 362 TRP cc_start: 0.7210 (t60) cc_final: 0.6220 (m-90) REVERT: D 8 GLU cc_start: 0.7957 (tp30) cc_final: 0.6743 (tp30) REVERT: D 11 ARG cc_start: 0.7976 (ttm-80) cc_final: 0.7717 (ttp80) REVERT: D 12 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.7396 (mt0) REVERT: D 118 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7570 (tt) REVERT: D 179 PHE cc_start: 0.8556 (t80) cc_final: 0.8172 (t80) outliers start: 27 outliers final: 16 residues processed: 157 average time/residue: 0.0842 time to fit residues: 19.4905 Evaluate side-chains 150 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 183 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 72 optimal weight: 4.9990 chunk 110 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 101 optimal weight: 0.2980 chunk 76 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.159299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.122685 restraints weight = 15808.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.127067 restraints weight = 9118.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.130070 restraints weight = 6410.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.132097 restraints weight = 5055.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.133342 restraints weight = 4302.176| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10544 Z= 0.175 Angle : 0.594 7.798 14269 Z= 0.309 Chirality : 0.044 0.199 1605 Planarity : 0.004 0.045 1737 Dihedral : 6.128 86.125 1349 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.77 % Allowed : 18.93 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.24), residues: 1235 helix: 1.30 (0.22), residues: 590 sheet: 0.65 (0.37), residues: 200 loop : -1.52 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 11 TYR 0.023 0.001 TYR B 150 PHE 0.034 0.002 PHE D 72 TRP 0.054 0.002 TRP D 31 HIS 0.005 0.001 HIS D 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 (10544) covalent geometry : angle 0.59406 / 0.31 (14269) hydrogen bonds : bond 0.04885 / 3.26 ( 498) hydrogen bonds : angle 4.56740 / 3.15 ( 1443) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 139 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7712 (tp) REVERT: A 184 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7943 (mt) REVERT: A 375 LYS cc_start: 0.8453 (tmmt) cc_final: 0.8152 (ttpp) REVERT: B 89 LYS cc_start: 0.8826 (ttmt) cc_final: 0.8329 (ttpp) REVERT: B 187 TYR cc_start: 0.8633 (p90) cc_final: 0.7938 (p90) REVERT: C 102 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7953 (pm20) REVERT: C 236 MET cc_start: 0.7983 (mmt) cc_final: 0.7660 (mmm) REVERT: D 8 GLU cc_start: 0.8040 (tp30) cc_final: 0.6865 (tp30) REVERT: D 11 ARG cc_start: 0.8015 (ttm-80) cc_final: 0.7742 (ttp80) REVERT: D 12 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.7486 (mt0) REVERT: D 37 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7863 (mm) REVERT: D 80 ARG cc_start: 0.8531 (ttp80) cc_final: 0.8123 (mtm180) REVERT: D 118 ILE cc_start: 0.7604 (OUTLIER) cc_final: 0.7404 (tt) REVERT: D 179 PHE cc_start: 0.8578 (t80) cc_final: 0.8192 (t80) outliers start: 31 outliers final: 20 residues processed: 156 average time/residue: 0.0879 time to fit residues: 20.4218 Evaluate side-chains 159 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 118 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 56 optimal weight: 0.0010 chunk 97 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 41 optimal weight: 0.2980 chunk 81 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 53 HIS D 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.165878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.132896 restraints weight = 15878.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.135889 restraints weight = 9775.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.138753 restraints weight = 6923.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.139060 restraints weight = 5827.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.139797 restraints weight = 5269.404| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10544 Z= 0.114 Angle : 0.538 8.020 14269 Z= 0.280 Chirality : 0.042 0.212 1605 Planarity : 0.004 0.038 1737 Dihedral : 5.689 78.141 1349 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.23 % Allowed : 19.73 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.25), residues: 1235 helix: 1.46 (0.22), residues: 598 sheet: 0.74 (0.37), residues: 200 loop : -1.59 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 11 TYR 0.017 0.001 TYR C 391 PHE 0.033 0.001 PHE D 175 TRP 0.048 0.002 TRP D 31 HIS 0.008 0.001 HIS B 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (10544) covalent geometry : angle 0.53751 / 0.28 (14269) hydrogen bonds : bond 0.04069 / 2.75 ( 498) hydrogen bonds : angle 4.39738 / 3.02 ( 1443) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7735 (tp) REVERT: A 184 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8098 (mt) REVERT: B 89 LYS cc_start: 0.8836 (ttmt) cc_final: 0.8369 (ttpp) REVERT: B 187 TYR cc_start: 0.8481 (p90) cc_final: 0.7912 (p90) REVERT: C 102 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8012 (pm20) REVERT: C 236 MET cc_start: 0.7969 (mmt) cc_final: 0.7578 (mmm) REVERT: D 8 GLU cc_start: 0.8026 (tp30) cc_final: 0.6903 (tp30) REVERT: D 12 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.7494 (mt0) REVERT: D 80 ARG cc_start: 0.8474 (ttp80) cc_final: 0.8027 (mtm180) REVERT: D 110 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8122 (mm-30) outliers start: 25 outliers final: 15 residues processed: 151 average time/residue: 0.0900 time to fit residues: 20.2315 Evaluate side-chains 146 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 65 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 85 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 66 optimal weight: 0.0030 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.164715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.131479 restraints weight = 15960.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.134174 restraints weight = 9991.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.137341 restraints weight = 7145.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.137600 restraints weight = 6013.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.139182 restraints weight = 5346.316| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10544 Z= 0.128 Angle : 0.556 7.977 14269 Z= 0.289 Chirality : 0.043 0.211 1605 Planarity : 0.004 0.040 1737 Dihedral : 5.543 75.155 1349 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.96 % Allowed : 20.18 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.25), residues: 1235 helix: 1.46 (0.22), residues: 598 sheet: 0.82 (0.37), residues: 200 loop : -1.54 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 11 TYR 0.016 0.001 TYR C 391 PHE 0.034 0.001 PHE D 175 TRP 0.041 0.002 TRP D 31 HIS 0.005 0.001 HIS D 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (10544) covalent geometry : angle 0.55627 / 0.29 (14269) hydrogen bonds : bond 0.04189 / 2.81 ( 498) hydrogen bonds : angle 4.37148 / 3.01 ( 1443) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7731 (tp) REVERT: A 184 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8096 (mt) REVERT: A 375 LYS cc_start: 0.8440 (tmmt) cc_final: 0.8077 (ttpp) REVERT: B 89 LYS cc_start: 0.8844 (ttmt) cc_final: 0.8378 (ttpp) REVERT: B 187 TYR cc_start: 0.8532 (p90) cc_final: 0.7934 (p90) REVERT: C 102 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.8004 (pm20) REVERT: C 236 MET cc_start: 0.7971 (mmt) cc_final: 0.7599 (mmm) REVERT: D 8 GLU cc_start: 0.7998 (tp30) cc_final: 0.7206 (tp30) REVERT: D 11 ARG cc_start: 0.8177 (ttp80) cc_final: 0.7916 (ttm-80) REVERT: D 12 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.7655 (mt0) REVERT: D 80 ARG cc_start: 0.8500 (ttp80) cc_final: 0.8107 (mtm180) REVERT: D 118 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7764 (tt) outliers start: 22 outliers final: 15 residues processed: 143 average time/residue: 0.0942 time to fit residues: 20.0112 Evaluate side-chains 147 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 172 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 28 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.161553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.128303 restraints weight = 15740.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.130775 restraints weight = 9878.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.133050 restraints weight = 7221.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.133373 restraints weight = 6374.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.135594 restraints weight = 5773.911| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10544 Z= 0.186 Angle : 0.610 10.571 14269 Z= 0.315 Chirality : 0.045 0.279 1605 Planarity : 0.004 0.045 1737 Dihedral : 5.720 78.362 1349 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.96 % Allowed : 20.18 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.24), residues: 1235 helix: 1.35 (0.22), residues: 590 sheet: 0.72 (0.37), residues: 200 loop : -1.58 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 11 TYR 0.023 0.001 TYR B 150 PHE 0.036 0.002 PHE D 175 TRP 0.048 0.002 TRP D 31 HIS 0.005 0.001 HIS D 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (10544) covalent geometry : angle 0.60982 / 0.31 (14269) hydrogen bonds : bond 0.04892 / 3.24 ( 498) hydrogen bonds : angle 4.49996 / 3.10 ( 1443) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7768 (tp) REVERT: A 184 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8070 (mt) REVERT: B 89 LYS cc_start: 0.8849 (ttmt) cc_final: 0.8388 (ttpp) REVERT: B 187 TYR cc_start: 0.8607 (p90) cc_final: 0.7838 (p90) REVERT: B 205 MET cc_start: 0.7248 (mmm) cc_final: 0.6874 (tpt) REVERT: C 102 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8073 (pm20) REVERT: D 8 GLU cc_start: 0.8019 (tp30) cc_final: 0.7231 (tp30) REVERT: D 11 ARG cc_start: 0.8218 (ttp80) cc_final: 0.7909 (ttm-80) REVERT: D 12 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7765 (mt0) REVERT: D 80 ARG cc_start: 0.8507 (ttp80) cc_final: 0.8025 (mtm180) REVERT: D 110 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8167 (mm-30) REVERT: D 118 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7586 (tt) outliers start: 22 outliers final: 17 residues processed: 150 average time/residue: 0.0926 time to fit residues: 20.7685 Evaluate side-chains 157 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 172 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 121 optimal weight: 0.4980 chunk 31 optimal weight: 10.0000 chunk 32 optimal weight: 0.2980 chunk 64 optimal weight: 0.0170 chunk 69 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 22 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.165686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.132596 restraints weight = 15913.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.136298 restraints weight = 9439.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.138841 restraints weight = 6537.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.139227 restraints weight = 5785.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.139547 restraints weight = 5076.283| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10544 Z= 0.113 Angle : 0.551 9.848 14269 Z= 0.285 Chirality : 0.042 0.252 1605 Planarity : 0.004 0.040 1737 Dihedral : 5.307 68.234 1349 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.88 % Allowed : 20.27 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.24), residues: 1235 helix: 1.48 (0.22), residues: 598 sheet: 0.88 (0.37), residues: 200 loop : -1.59 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 11 TYR 0.017 0.001 TYR C 391 PHE 0.034 0.001 PHE D 175 TRP 0.044 0.002 TRP D 31 HIS 0.004 0.001 HIS D 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (10544) covalent geometry : angle 0.55128 / 0.28 (14269) hydrogen bonds : bond 0.03962 / 2.66 ( 498) hydrogen bonds : angle 4.33270 / 2.98 ( 1443) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1599.06 seconds wall clock time: 28 minutes 31.96 seconds (1711.96 seconds total)