Starting phenix.real_space_refine on Thu Feb 5 20:14:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dx3_47279/02_2026/9dx3_47279_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dx3_47279/02_2026/9dx3_47279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dx3_47279/02_2026/9dx3_47279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dx3_47279/02_2026/9dx3_47279.map" model { file = "/net/cci-nas-00/data/ceres_data/9dx3_47279/02_2026/9dx3_47279_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dx3_47279/02_2026/9dx3_47279_trim.cif" } resolution = 2.94 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= 0.024 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: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 79 5.16 5 C 12322 2.51 5 N 3435 2.21 5 O 3652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19504 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2390 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 17, 'TRANS': 288} Chain: "B" Number of atoms: 2419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2419 Classifications: {'peptide': 310} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 291} Chain: "C" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2450 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 19, 'TRANS': 294} Chain: "D" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2300 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 17, 'TRANS': 276} Chain breaks: 1 Chain: "E" Number of atoms: 2419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2419 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 18, 'TRANS': 291} Chain: "F" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2424 Classifications: {'peptide': 311} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 292} Chain: "G" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2424 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 18, 'TRANS': 292} Chain: "H" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1347 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 13, 'TRANS': 159} Chain: "I" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1115 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.15, per 1000 atoms: 0.21 Number of scatterers: 19504 At special positions: 0 Unit cell: (119.72, 140.89, 143.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 79 16.00 P 16 15.00 O 3652 8.00 N 3435 7.00 C 12322 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: 1.71 Conformation dependent library (CDL) restraints added in 721.6 milliseconds 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4556 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 23 sheets defined 54.6% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 27 through 31 Processing helix chain 'A' and resid 34 through 52 removed outlier: 3.526A pdb=" N ILE A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 79 Processing helix chain 'A' and resid 93 through 103 removed outlier: 4.403A pdb=" N LEU A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 118 Processing helix chain 'A' and resid 119 through 133 removed outlier: 3.901A pdb=" N VAL A 125 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 185 through 201 removed outlier: 3.847A pdb=" N TYR A 191 " --> pdb=" O PRO A 187 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 192 " --> pdb=" O ASP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.821A pdb=" N GLU A 211 " --> pdb=" O ASP A 207 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A 212 " --> pdb=" O GLY A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 237 Processing helix chain 'A' and resid 245 through 255 Processing helix chain 'A' and resid 262 through 274 Processing helix chain 'A' and resid 284 through 291 removed outlier: 4.509A pdb=" N ALA A 288 " --> pdb=" O ASP A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 301 through 308 removed outlier: 3.939A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 328 Processing helix chain 'B' and resid 27 through 31 Processing helix chain 'B' and resid 34 through 52 removed outlier: 3.510A pdb=" N ILE B 43 " --> pdb=" O SER B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 80 Processing helix chain 'B' and resid 93 through 103 removed outlier: 3.623A pdb=" N LEU B 97 " --> pdb=" O LYS B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 118 Processing helix chain 'B' and resid 119 through 133 removed outlier: 3.944A pdb=" N VAL B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Proline residue: B 128 - end of helix Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 185 through 201 Processing helix chain 'B' and resid 205 through 215 Processing helix chain 'B' and resid 219 through 236 Processing helix chain 'B' and resid 249 through 254 removed outlier: 3.674A pdb=" N LEU B 254 " --> pdb=" O ALA B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 270 Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 293 through 300 Processing helix chain 'B' and resid 301 through 308 removed outlier: 3.506A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 329 removed outlier: 3.802A pdb=" N TRP B 325 " --> pdb=" O THR B 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 51 Processing helix chain 'C' and resid 67 through 79 Processing helix chain 'C' and resid 93 through 104 removed outlier: 3.722A pdb=" N LEU C 97 " --> pdb=" O LYS C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 118 Processing helix chain 'C' and resid 119 through 132 removed outlier: 3.536A pdb=" N VAL C 125 " --> pdb=" O VAL C 121 " (cutoff:3.500A) Proline residue: C 128 - end of helix Processing helix chain 'C' and resid 185 through 201 Processing helix chain 'C' and resid 205 through 215 Processing helix chain 'C' and resid 219 through 238 Processing helix chain 'C' and resid 243 through 254 removed outlier: 3.898A pdb=" N ALA C 247 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLN C 249 " --> pdb=" O ASP C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 275 Processing helix chain 'C' and resid 285 through 290 removed outlier: 3.583A pdb=" N ALA C 289 " --> pdb=" O ASN C 285 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 285 through 290' Processing helix chain 'C' and resid 293 through 298 Processing helix chain 'C' and resid 301 through 308 removed outlier: 3.845A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 328 Processing helix chain 'D' and resid 27 through 31 Processing helix chain 'D' and resid 34 through 52 removed outlier: 3.896A pdb=" N GLN D 40 " --> pdb=" O GLN D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 79 Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 122 through 133 Proline residue: D 128 - end of helix Processing helix chain 'D' and resid 163 through 168 removed outlier: 3.562A pdb=" N SER D 166 " --> pdb=" O ARG D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 175 Processing helix chain 'D' and resid 185 through 201 Processing helix chain 'D' and resid 205 through 215 removed outlier: 3.509A pdb=" N ALA D 209 " --> pdb=" O SER D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 237 Processing helix chain 'D' and resid 245 through 251 Processing helix chain 'D' and resid 262 through 275 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 301 through 308 removed outlier: 3.771A pdb=" N LEU D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 328 removed outlier: 3.753A pdb=" N PHE D 328 " --> pdb=" O ALA D 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 31 Processing helix chain 'E' and resid 34 through 51 removed outlier: 3.538A pdb=" N PHE E 44 " --> pdb=" O GLN E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 79 removed outlier: 3.813A pdb=" N MET E 79 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 103 removed outlier: 3.789A pdb=" N LEU E 97 " --> pdb=" O LYS E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 118 Processing helix chain 'E' and resid 119 through 132 removed outlier: 3.645A pdb=" N VAL E 125 " --> pdb=" O VAL E 121 " (cutoff:3.500A) Proline residue: E 128 - end of helix Processing helix chain 'E' and resid 164 through 169 removed outlier: 4.389A pdb=" N THR E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 201 Processing helix chain 'E' and resid 205 through 215 removed outlier: 3.586A pdb=" N ARG E 215 " --> pdb=" O GLU E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 238 Processing helix chain 'E' and resid 243 through 254 Processing helix chain 'E' and resid 262 through 275 Processing helix chain 'E' and resid 287 through 291 removed outlier: 3.523A pdb=" N ILE E 290 " --> pdb=" O ALA E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 300 Processing helix chain 'E' and resid 301 through 308 removed outlier: 3.955A pdb=" N LEU E 305 " --> pdb=" O LEU E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 329 removed outlier: 4.018A pdb=" N TRP E 325 " --> pdb=" O THR E 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 31 removed outlier: 3.521A pdb=" N TYR F 31 " --> pdb=" O LEU F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 51 removed outlier: 3.512A pdb=" N ARG F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 79 Processing helix chain 'F' and resid 93 through 103 removed outlier: 3.827A pdb=" N LEU F 97 " --> pdb=" O LYS F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 118 Processing helix chain 'F' and resid 119 through 133 removed outlier: 3.919A pdb=" N VAL F 125 " --> pdb=" O VAL F 121 " (cutoff:3.500A) Proline residue: F 128 - end of helix Processing helix chain 'F' and resid 168 through 173 Processing helix chain 'F' and resid 185 through 201 Processing helix chain 'F' and resid 205 through 215 removed outlier: 3.639A pdb=" N ARG F 215 " --> pdb=" O GLU F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 237 removed outlier: 3.712A pdb=" N ARG F 228 " --> pdb=" O ASN F 224 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 253 removed outlier: 4.313A pdb=" N ALA F 248 " --> pdb=" O ALA F 244 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP F 252 " --> pdb=" O ALA F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 275 Processing helix chain 'F' and resid 286 through 291 removed outlier: 3.996A pdb=" N ALA F 289 " --> pdb=" O LEU F 286 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE F 290 " --> pdb=" O ALA F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 300 Processing helix chain 'F' and resid 301 through 308 removed outlier: 4.038A pdb=" N LEU F 305 " --> pdb=" O LEU F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 329 removed outlier: 3.710A pdb=" N TRP F 325 " --> pdb=" O THR F 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 31 Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.544A pdb=" N ILE G 43 " --> pdb=" O SER G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 79 Processing helix chain 'G' and resid 93 through 104 removed outlier: 3.808A pdb=" N LEU G 97 " --> pdb=" O LYS G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 118 Processing helix chain 'G' and resid 119 through 133 removed outlier: 4.064A pdb=" N VAL G 125 " --> pdb=" O VAL G 121 " (cutoff:3.500A) Proline residue: G 128 - end of helix Processing helix chain 'G' and resid 163 through 168 Processing helix chain 'G' and resid 169 through 175 Processing helix chain 'G' and resid 185 through 201 Processing helix chain 'G' and resid 205 through 214 removed outlier: 3.641A pdb=" N LEU G 210 " --> pdb=" O ASP G 206 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU G 211 " --> pdb=" O ASP G 207 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL G 212 " --> pdb=" O GLY G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 238 Processing helix chain 'G' and resid 243 through 249 removed outlier: 3.831A pdb=" N ILE G 246 " --> pdb=" O SER G 243 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 274 Processing helix chain 'G' and resid 286 through 291 removed outlier: 3.509A pdb=" N ILE G 290 " --> pdb=" O ALA G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 300 Processing helix chain 'G' and resid 301 through 308 removed outlier: 3.835A pdb=" N LEU G 305 " --> pdb=" O LEU G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 329 removed outlier: 3.554A pdb=" N TRP G 325 " --> pdb=" O THR G 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 31 Processing helix chain 'H' and resid 34 through 52 Processing helix chain 'H' and resid 67 through 80 Processing helix chain 'H' and resid 93 through 103 removed outlier: 4.056A pdb=" N LEU H 97 " --> pdb=" O LYS H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 118 removed outlier: 3.899A pdb=" N LEU H 118 " --> pdb=" O ILE H 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 115 through 118' Processing helix chain 'H' and resid 119 through 132 Proline residue: H 128 - end of helix Processing helix chain 'H' and resid 168 through 174 removed outlier: 3.821A pdb=" N ARG H 174 " --> pdb=" O PRO H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 195 Processing helix chain 'I' and resid 37 through 52 Processing helix chain 'I' and resid 67 through 80 Processing helix chain 'I' and resid 93 through 103 removed outlier: 3.751A pdb=" N LEU I 97 " --> pdb=" O LYS I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 118 Processing helix chain 'I' and resid 119 through 133 removed outlier: 3.685A pdb=" N VAL I 125 " --> pdb=" O VAL I 121 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU I 126 " --> pdb=" O VAL I 122 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR I 127 " --> pdb=" O GLU I 123 " (cutoff:3.500A) Proline residue: I 128 - end of helix Processing helix chain 'I' and resid 163 through 167 Processing helix chain 'I' and resid 168 through 173 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 87 removed outlier: 6.252A pdb=" N ARG A 84 " --> pdb=" O PHE A 111 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ASP A 113 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR A 86 " --> pdb=" O ASP A 113 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A 161 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU A 59 " --> pdb=" O GLN A 179 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 137 Processing sheet with id=AA3, first strand: chain 'A' and resid 311 through 313 Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 86 removed outlier: 6.380A pdb=" N ARG B 84 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ASP B 113 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR B 86 " --> pdb=" O ASP B 113 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU B 59 " --> pdb=" O GLN B 179 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 134 through 138 Processing sheet with id=AA6, first strand: chain 'B' and resid 312 through 313 Processing sheet with id=AA7, first strand: chain 'C' and resid 83 through 87 removed outlier: 6.069A pdb=" N ARG C 84 " --> pdb=" O PHE C 111 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ASP C 113 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR C 86 " --> pdb=" O ASP C 113 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU C 59 " --> pdb=" O GLN C 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 134 through 138 Processing sheet with id=AA9, first strand: chain 'D' and resid 58 through 61 Processing sheet with id=AB1, first strand: chain 'D' and resid 83 through 87 Processing sheet with id=AB2, first strand: chain 'D' and resid 311 through 312 Processing sheet with id=AB3, first strand: chain 'E' and resid 83 through 87 removed outlier: 6.377A pdb=" N ARG E 84 " --> pdb=" O PHE E 111 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ASP E 113 " --> pdb=" O ARG E 84 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR E 86 " --> pdb=" O ASP E 113 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU E 110 " --> pdb=" O ILE E 158 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ALA E 160 " --> pdb=" O LEU E 110 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE E 112 " --> pdb=" O ALA E 160 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU E 59 " --> pdb=" O GLN E 179 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 137 through 139 Processing sheet with id=AB5, first strand: chain 'E' and resid 311 through 313 Processing sheet with id=AB6, first strand: chain 'F' and resid 83 through 87 removed outlier: 6.432A pdb=" N ARG F 84 " --> pdb=" O PHE F 111 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ASP F 113 " --> pdb=" O ARG F 84 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR F 86 " --> pdb=" O ASP F 113 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASP F 108 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE F 158 " --> pdb=" O ASP F 108 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU F 110 " --> pdb=" O ILE F 158 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ALA F 160 " --> pdb=" O LEU F 110 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE F 112 " --> pdb=" O ALA F 160 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU F 59 " --> pdb=" O GLN F 179 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 134 through 139 Processing sheet with id=AB8, first strand: chain 'G' and resid 83 through 87 removed outlier: 6.386A pdb=" N ARG G 84 " --> pdb=" O PHE G 111 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASP G 113 " --> pdb=" O ARG G 84 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR G 86 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASP G 108 " --> pdb=" O THR G 156 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE G 158 " --> pdb=" O ASP G 108 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU G 110 " --> pdb=" O ILE G 158 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ALA G 160 " --> pdb=" O LEU G 110 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE G 112 " --> pdb=" O ALA G 160 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU G 59 " --> pdb=" O GLN G 179 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 134 through 139 Processing sheet with id=AC1, first strand: chain 'G' and resid 311 through 313 Processing sheet with id=AC2, first strand: chain 'H' and resid 83 through 87 removed outlier: 6.287A pdb=" N LEU H 59 " --> pdb=" O GLN H 179 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 134 through 138 Processing sheet with id=AC4, first strand: chain 'I' and resid 83 through 87 removed outlier: 6.303A pdb=" N ARG I 84 " --> pdb=" O PHE I 111 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ASP I 113 " --> pdb=" O ARG I 84 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR I 86 " --> pdb=" O ASP I 113 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU I 110 " --> pdb=" O ILE I 158 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ALA I 160 " --> pdb=" O LEU I 110 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE I 112 " --> pdb=" O ALA I 160 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU I 59 " --> pdb=" O GLN I 179 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 134 through 138 892 hydrogen bonds defined for protein. 2508 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: 3.40 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.42: 7923 1.42 - 1.61: 11757 1.61 - 1.80: 124 1.80 - 1.99: 66 1.99 - 2.18: 1 Bond restraints: 19871 Sorted by residual: bond pdb=" C MET A 253 " pdb=" N ASN A 255 " ideal model delta sigma weight residual 1.333 2.185 -0.851 1.43e-02 4.89e+03 3.54e+03 bond pdb=" C2' ADP A 401 " pdb=" C3' ADP A 401 " ideal model delta sigma weight residual 1.524 1.280 0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C2' ADP D 401 " pdb=" C3' ADP D 401 " ideal model delta sigma weight residual 1.524 1.283 0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" C2' ADP C 401 " pdb=" C3' ADP C 401 " ideal model delta sigma weight residual 1.524 1.284 0.240 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C2' ADP F 401 " pdb=" C3' ADP F 401 " ideal model delta sigma weight residual 1.524 1.287 0.237 2.00e-02 2.50e+03 1.40e+02 ... (remaining 19866 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.18: 26874 6.18 - 12.37: 60 12.37 - 18.55: 19 18.55 - 24.74: 8 24.74 - 30.92: 7 Bond angle restraints: 26968 Sorted by residual: angle pdb=" C2' ADP H 401 " pdb=" C1' ADP H 401 " pdb=" N9 ADP H 401 " ideal model delta sigma weight residual 109.47 140.39 -30.92 3.00e+00 1.11e-01 1.06e+02 angle pdb=" CA MET A 253 " pdb=" C MET A 253 " pdb=" N ASN A 255 " ideal model delta sigma weight residual 117.72 104.34 13.38 1.31e+00 5.83e-01 1.04e+02 angle pdb=" C2' ADP F 401 " pdb=" C1' ADP F 401 " pdb=" N9 ADP F 401 " ideal model delta sigma weight residual 109.47 139.97 -30.50 3.00e+00 1.11e-01 1.03e+02 angle pdb=" C2' ADP C 401 " pdb=" C1' ADP C 401 " pdb=" N9 ADP C 401 " ideal model delta sigma weight residual 109.47 139.10 -29.63 3.00e+00 1.11e-01 9.76e+01 angle pdb=" C2' ADP G 401 " pdb=" C1' ADP G 401 " pdb=" N9 ADP G 401 " ideal model delta sigma weight residual 109.47 138.99 -29.52 3.00e+00 1.11e-01 9.68e+01 ... (remaining 26963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.53: 11891 35.53 - 71.06: 183 71.06 - 106.59: 26 106.59 - 142.12: 9 142.12 - 177.65: 3 Dihedral angle restraints: 12112 sinusoidal: 5035 harmonic: 7077 Sorted by residual: dihedral pdb=" O2A ADP G 401 " pdb=" O3A ADP G 401 " pdb=" PA ADP G 401 " pdb=" PB ADP G 401 " ideal model delta sinusoidal sigma weight residual 300.00 122.35 177.65 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP G 401 " pdb=" O5' ADP G 401 " pdb=" PA ADP G 401 " pdb=" O2A ADP G 401 " ideal model delta sinusoidal sigma weight residual -60.00 106.04 -166.04 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 157.14 142.86 1 2.00e+01 2.50e-03 4.31e+01 ... (remaining 12109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.982: 3044 0.982 - 1.964: 0 1.964 - 2.946: 0 2.946 - 3.928: 0 3.928 - 4.910: 24 Chirality restraints: 3068 Sorted by residual: chirality pdb=" C2' ADP H 401 " pdb=" C1' ADP H 401 " pdb=" C3' ADP H 401 " pdb=" O2' ADP H 401 " both_signs ideal model delta sigma weight residual False -2.51 2.40 -4.91 2.00e-01 2.50e+01 6.03e+02 chirality pdb=" C2' ADP G 401 " pdb=" C1' ADP G 401 " pdb=" C3' ADP G 401 " pdb=" O2' ADP G 401 " both_signs ideal model delta sigma weight residual False -2.51 2.38 -4.89 2.00e-01 2.50e+01 5.98e+02 chirality pdb=" C2' ADP F 401 " pdb=" C1' ADP F 401 " pdb=" C3' ADP F 401 " pdb=" O2' ADP F 401 " both_signs ideal model delta sigma weight residual False -2.51 2.38 -4.89 2.00e-01 2.50e+01 5.98e+02 ... (remaining 3065 not shown) Planarity restraints: 3520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 253 " 0.071 2.00e-02 2.50e+03 1.39e-01 1.94e+02 pdb=" C MET A 253 " -0.239 2.00e-02 2.50e+03 pdb=" O MET A 253 " 0.113 2.00e-02 2.50e+03 pdb=" N ASN A 255 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 279 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO B 280 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 280 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 280 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 228 " -0.150 9.50e-02 1.11e+02 6.76e-02 3.19e+00 pdb=" NE ARG E 228 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG E 228 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG E 228 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG E 228 " -0.002 2.00e-02 2.50e+03 ... (remaining 3517 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 245 2.63 - 3.20: 17880 3.20 - 3.76: 29860 3.76 - 4.33: 42181 4.33 - 4.90: 69947 Nonbonded interactions: 160113 Sorted by model distance: nonbonded pdb=" OG SER B 243 " pdb=" OD1 ASP B 245 " model vdw 2.062 3.040 nonbonded pdb=" NH2 ARG B 51 " pdb=" OD1 ASP C 232 " model vdw 2.107 3.120 nonbonded pdb=" OE2 GLU E 302 " pdb=" NH2 ARG E 313 " model vdw 2.173 3.120 nonbonded pdb=" O GLY B 309 " pdb=" OG1 THR B 321 " model vdw 2.188 3.040 nonbonded pdb=" NE2 GLN C 40 " pdb=" O MET D 253 " model vdw 2.193 3.120 ... (remaining 160108 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 23 through 135 or resid 153 through 401)) selection = (chain 'B' and (resid 23 through 135 or resid 153 through 253 or resid 255 throu \ gh 328 or resid 401)) selection = (chain 'C' and (resid 23 through 135 or resid 153 through 253 or resid 255 throu \ gh 328 or resid 401)) selection = (chain 'D' and (resid 23 through 253 or resid 255 through 328 or resid 401)) selection = (chain 'E' and (resid 23 through 135 or resid 153 through 253 or resid 255 throu \ gh 328 or resid 401)) selection = (chain 'F' and (resid 23 through 135 or resid 153 through 253 or resid 255 throu \ gh 328 or resid 401)) selection = (chain 'G' and (resid 23 through 135 or resid 153 through 253 or resid 255 throu \ gh 328 or resid 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.790 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 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 : 0.010 0.851 19871 Z= 0.575 Angle : 1.017 30.921 26968 Z= 0.399 Chirality : 0.418 4.910 3068 Planarity : 0.005 0.139 3520 Dihedral : 14.880 177.646 7556 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.16 % Favored : 95.80 % Rotamer: Outliers : 0.05 % Allowed : 0.00 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: 0.57 (0.18), residues: 2453 helix: 1.00 (0.16), residues: 1206 sheet: 0.38 (0.27), residues: 432 loop : -0.42 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 228 TYR 0.007 0.001 TYR F 191 PHE 0.016 0.001 PHE F 276 TRP 0.009 0.001 TRP G 325 HIS 0.007 0.001 HIS E 116 Details of bonding type rmsd covalent geometry : bond 0.00993 (19871) covalent geometry : angle 1.01661 (26968) hydrogen bonds : bond 0.16226 ( 892) hydrogen bonds : angle 6.81510 ( 2508) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 431 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 MET cc_start: 0.7166 (mtp) cc_final: 0.6851 (mtp) REVERT: B 204 MET cc_start: 0.7635 (ttm) cc_final: 0.6991 (ptm) REVERT: C 318 ARG cc_start: 0.7280 (mtt90) cc_final: 0.7043 (mpt180) REVERT: D 41 MET cc_start: 0.2637 (mmp) cc_final: 0.2387 (mmp) REVERT: D 130 MET cc_start: 0.5443 (tpp) cc_final: 0.5130 (tpp) REVERT: D 182 GLU cc_start: 0.6732 (mp0) cc_final: 0.6419 (mp0) REVERT: D 195 ARG cc_start: 0.6903 (ttt-90) cc_final: 0.6377 (tpt170) REVERT: D 299 ASP cc_start: 0.6428 (m-30) cc_final: 0.6124 (m-30) REVERT: D 314 THR cc_start: 0.5914 (t) cc_final: 0.5658 (t) REVERT: E 252 ASP cc_start: 0.7710 (m-30) cc_final: 0.7454 (m-30) REVERT: F 117 ARG cc_start: 0.7704 (mtp85) cc_final: 0.7051 (mtp85) REVERT: G 124 GLU cc_start: 0.7880 (pt0) cc_final: 0.7672 (pt0) REVERT: H 84 ARG cc_start: 0.6841 (ttt90) cc_final: 0.6601 (ttt90) REVERT: H 133 TYR cc_start: 0.8300 (m-80) cc_final: 0.7693 (m-80) outliers start: 1 outliers final: 1 residues processed: 431 average time/residue: 0.6836 time to fit residues: 325.0382 Evaluate side-chains 400 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 399 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 235 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN D 40 GLN ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN E 185 GLN E 312 GLN F 255 ASN F 308 GLN F 312 GLN G 34 GLN G 134 GLN I 107 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.170545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.141208 restraints weight = 26042.141| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.02 r_work: 0.3610 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19871 Z= 0.177 Angle : 0.726 9.510 26968 Z= 0.331 Chirality : 0.044 0.262 3068 Planarity : 0.005 0.052 3520 Dihedral : 10.153 175.555 2814 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.71 % Favored : 96.21 % Rotamer: Outliers : 1.57 % Allowed : 9.42 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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 (0.18), residues: 2455 helix: 0.80 (0.15), residues: 1211 sheet: 0.70 (0.27), residues: 401 loop : -0.40 (0.23), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 318 TYR 0.011 0.001 TYR H 191 PHE 0.013 0.001 PHE A 61 TRP 0.005 0.001 TRP G 325 HIS 0.004 0.001 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00418 (19871) covalent geometry : angle 0.72621 (26968) hydrogen bonds : bond 0.04416 ( 892) hydrogen bonds : angle 5.51343 ( 2508) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 402 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 MET cc_start: 0.7378 (mtp) cc_final: 0.7054 (mtp) REVERT: A 266 ARG cc_start: 0.7858 (ttp80) cc_final: 0.7356 (ttp80) REVERT: B 204 MET cc_start: 0.7710 (ttm) cc_final: 0.7061 (ptm) REVERT: B 259 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7695 (mt-10) REVERT: C 319 MET cc_start: 0.7498 (tpp) cc_final: 0.7187 (mmt) REVERT: D 41 MET cc_start: 0.2717 (mmp) cc_final: 0.2308 (mmp) REVERT: D 130 MET cc_start: 0.5478 (tpp) cc_final: 0.5162 (tpp) REVERT: D 182 GLU cc_start: 0.6943 (mp0) cc_final: 0.6697 (mp0) REVERT: D 200 MET cc_start: 0.7010 (mtm) cc_final: 0.6727 (ttm) REVERT: D 266 ARG cc_start: 0.7036 (ttm-80) cc_final: 0.6569 (ttm-80) REVERT: D 318 ARG cc_start: 0.6122 (mmt90) cc_final: 0.5833 (mmt-90) REVERT: E 257 ASP cc_start: 0.8061 (p0) cc_final: 0.7830 (p0) REVERT: E 319 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7540 (tpp) REVERT: E 321 THR cc_start: 0.8338 (t) cc_final: 0.8121 (p) REVERT: F 78 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7957 (mt-10) REVERT: G 311 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7934 (mp) REVERT: H 41 MET cc_start: 0.8843 (mmm) cc_final: 0.8618 (mmm) outliers start: 32 outliers final: 12 residues processed: 412 average time/residue: 0.6985 time to fit residues: 318.2058 Evaluate side-chains 416 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 401 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain H residue 86 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 56 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 chunk 214 optimal weight: 0.5980 chunk 156 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 228 optimal weight: 0.3980 chunk 142 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 222 optimal weight: 1.9990 chunk 189 optimal weight: 0.0870 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN B 312 GLN C 285 ASN D 40 GLN ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN F 179 GLN F 255 ASN F 312 GLN G 134 GLN I 107 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.172231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.143039 restraints weight = 26095.943| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.04 r_work: 0.3627 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19871 Z= 0.133 Angle : 0.649 9.379 26968 Z= 0.296 Chirality : 0.042 0.162 3068 Planarity : 0.005 0.054 3520 Dihedral : 9.827 177.055 2811 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.91 % Favored : 96.05 % Rotamer: Outliers : 1.86 % Allowed : 12.06 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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 (0.18), residues: 2455 helix: 0.76 (0.15), residues: 1214 sheet: 0.73 (0.27), residues: 399 loop : -0.31 (0.23), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 117 TYR 0.009 0.001 TYR G 133 PHE 0.011 0.001 PHE F 233 TRP 0.006 0.001 TRP G 325 HIS 0.006 0.001 HIS I 57 Details of bonding type rmsd covalent geometry : bond 0.00307 (19871) covalent geometry : angle 0.64859 (26968) hydrogen bonds : bond 0.03668 ( 892) hydrogen bonds : angle 5.14838 ( 2508) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 390 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 MET cc_start: 0.7364 (mtp) cc_final: 0.7052 (mtp) REVERT: A 266 ARG cc_start: 0.7876 (ttp80) cc_final: 0.7537 (ttp80) REVERT: B 204 MET cc_start: 0.7626 (ttm) cc_final: 0.6983 (ptm) REVERT: C 32 VAL cc_start: 0.8135 (p) cc_final: 0.7763 (m) REVERT: C 132 ASP cc_start: 0.7795 (p0) cc_final: 0.7570 (p0) REVERT: C 173 ASP cc_start: 0.7159 (m-30) cc_final: 0.6907 (m-30) REVERT: C 318 ARG cc_start: 0.7530 (mtt90) cc_final: 0.7230 (mpt180) REVERT: C 319 MET cc_start: 0.7452 (tpp) cc_final: 0.7131 (mmp) REVERT: D 130 MET cc_start: 0.5566 (tpp) cc_final: 0.5200 (tpp) REVERT: D 200 MET cc_start: 0.7066 (mtm) cc_final: 0.6746 (ttm) REVERT: D 266 ARG cc_start: 0.7188 (ttm-80) cc_final: 0.6805 (ttm-80) REVERT: D 318 ARG cc_start: 0.6241 (mmt90) cc_final: 0.5968 (mmt-90) REVERT: E 130 MET cc_start: 0.7152 (mmm) cc_final: 0.5413 (tmm) REVERT: E 146 ARG cc_start: 0.8029 (mtm180) cc_final: 0.7828 (mtm180) REVERT: H 41 MET cc_start: 0.8824 (mmm) cc_final: 0.8582 (mmp) outliers start: 38 outliers final: 11 residues processed: 402 average time/residue: 0.7071 time to fit residues: 314.3447 Evaluate side-chains 395 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 384 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain H residue 30 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 85 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 101 optimal weight: 0.0870 chunk 129 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 29 optimal weight: 0.0060 chunk 229 optimal weight: 1.9990 chunk 237 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 overall best weight: 0.4774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN D 40 GLN ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 ASN E 40 GLN F 179 GLN F 255 ASN F 312 GLN I 107 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.175682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.146650 restraints weight = 25917.149| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.01 r_work: 0.3631 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19871 Z= 0.128 Angle : 0.638 9.338 26968 Z= 0.290 Chirality : 0.041 0.157 3068 Planarity : 0.005 0.055 3520 Dihedral : 9.676 178.333 2811 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.99 % Favored : 95.97 % Rotamer: Outliers : 2.11 % Allowed : 13.83 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: 0.60 (0.17), residues: 2455 helix: 0.83 (0.15), residues: 1218 sheet: 0.77 (0.26), residues: 403 loop : -0.28 (0.23), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 172 TYR 0.006 0.001 TYR G 133 PHE 0.012 0.001 PHE C 61 TRP 0.005 0.001 TRP G 325 HIS 0.004 0.000 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00298 (19871) covalent geometry : angle 0.63787 (26968) hydrogen bonds : bond 0.03465 ( 892) hydrogen bonds : angle 5.01340 ( 2508) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 385 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 MET cc_start: 0.7350 (mtp) cc_final: 0.7020 (mtp) REVERT: B 204 MET cc_start: 0.7642 (ttm) cc_final: 0.6999 (ptm) REVERT: B 259 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7752 (mt-10) REVERT: B 319 MET cc_start: 0.7432 (ttm) cc_final: 0.7190 (tpp) REVERT: C 32 VAL cc_start: 0.8204 (p) cc_final: 0.7878 (m) REVERT: C 49 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7668 (mtpt) REVERT: C 173 ASP cc_start: 0.7158 (m-30) cc_final: 0.6915 (m-30) REVERT: C 318 ARG cc_start: 0.7404 (mtt90) cc_final: 0.7096 (mmt180) REVERT: C 319 MET cc_start: 0.7377 (tpp) cc_final: 0.7080 (mmp) REVERT: D 130 MET cc_start: 0.5546 (tpp) cc_final: 0.5264 (tpp) REVERT: D 200 MET cc_start: 0.6997 (mtm) cc_final: 0.6698 (ttm) REVERT: D 266 ARG cc_start: 0.7151 (ttm-80) cc_final: 0.6808 (ttm-80) REVERT: D 318 ARG cc_start: 0.6250 (mmt90) cc_final: 0.5970 (mmt-90) REVERT: F 78 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7493 (tt0) REVERT: G 203 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7198 (tm-30) REVERT: H 41 MET cc_start: 0.8843 (mmm) cc_final: 0.8616 (mmm) REVERT: H 100 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7674 (mtm) outliers start: 43 outliers final: 14 residues processed: 402 average time/residue: 0.6616 time to fit residues: 294.4622 Evaluate side-chains 396 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 379 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 295 GLU Chi-restraints excluded: chain H residue 30 GLU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain I residue 41 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 222 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 156 optimal weight: 0.0170 chunk 120 optimal weight: 5.9990 chunk 202 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 133 optimal weight: 0.0020 chunk 218 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 228 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.5828 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 312 GLN D 40 GLN ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 HIS F 179 GLN F 255 ASN F 312 GLN I 107 HIS I 116 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.172205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.142361 restraints weight = 25627.637| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.08 r_work: 0.3616 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19871 Z= 0.138 Angle : 0.642 10.160 26968 Z= 0.291 Chirality : 0.042 0.152 3068 Planarity : 0.005 0.056 3520 Dihedral : 9.604 179.049 2811 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.83 % Favored : 96.13 % Rotamer: Outliers : 2.06 % Allowed : 15.35 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: 0.60 (0.17), residues: 2455 helix: 0.82 (0.15), residues: 1220 sheet: 0.85 (0.26), residues: 393 loop : -0.29 (0.23), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 225 TYR 0.006 0.001 TYR F 31 PHE 0.014 0.001 PHE F 276 TRP 0.006 0.001 TRP F 325 HIS 0.004 0.001 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00328 (19871) covalent geometry : angle 0.64170 (26968) hydrogen bonds : bond 0.03484 ( 892) hydrogen bonds : angle 4.95749 ( 2508) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 383 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ASP cc_start: 0.7838 (m-30) cc_final: 0.6763 (m-30) REVERT: A 264 MET cc_start: 0.7364 (mtp) cc_final: 0.7030 (mtp) REVERT: B 192 ILE cc_start: 0.8049 (mt) cc_final: 0.7832 (mp) REVERT: B 204 MET cc_start: 0.7628 (ttm) cc_final: 0.7008 (ptm) REVERT: B 259 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7778 (mt-10) REVERT: B 319 MET cc_start: 0.7525 (ttm) cc_final: 0.7246 (tpp) REVERT: C 32 VAL cc_start: 0.8207 (p) cc_final: 0.7922 (m) REVERT: C 49 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7736 (mtpt) REVERT: C 318 ARG cc_start: 0.7419 (mtt90) cc_final: 0.7087 (mmt180) REVERT: C 319 MET cc_start: 0.7342 (tpp) cc_final: 0.7088 (mmp) REVERT: D 130 MET cc_start: 0.5560 (tpp) cc_final: 0.5268 (tpp) REVERT: D 200 MET cc_start: 0.7068 (mtm) cc_final: 0.6762 (ttm) REVERT: D 266 ARG cc_start: 0.7167 (ttm-80) cc_final: 0.6851 (ttm-80) REVERT: D 318 ARG cc_start: 0.6303 (mmt90) cc_final: 0.5995 (mmt-90) REVERT: E 130 MET cc_start: 0.7209 (mmm) cc_final: 0.6813 (mmm) REVERT: E 133 TYR cc_start: 0.7863 (m-80) cc_final: 0.7033 (m-80) REVERT: E 146 ARG cc_start: 0.8105 (mtm180) cc_final: 0.7870 (mtm180) REVERT: E 284 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.6901 (t0) REVERT: G 172 ARG cc_start: 0.6918 (tmt-80) cc_final: 0.6628 (tmt-80) REVERT: G 203 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7135 (tm-30) REVERT: H 100 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7676 (mtm) outliers start: 42 outliers final: 19 residues processed: 401 average time/residue: 0.6705 time to fit residues: 297.6984 Evaluate side-chains 400 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 377 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 295 GLU Chi-restraints excluded: chain H residue 30 GLU Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain I residue 41 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 91 optimal weight: 3.9990 chunk 234 optimal weight: 0.4980 chunk 11 optimal weight: 3.9990 chunk 232 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 213 optimal weight: 4.9990 chunk 197 optimal weight: 0.4980 chunk 12 optimal weight: 0.4980 chunk 48 optimal weight: 0.6980 chunk 228 optimal weight: 0.8980 chunk 30 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN D 40 GLN ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 GLN F 255 ASN I 116 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.172169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.142754 restraints weight = 25569.761| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.06 r_work: 0.3628 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19871 Z= 0.131 Angle : 0.635 11.816 26968 Z= 0.288 Chirality : 0.041 0.154 3068 Planarity : 0.005 0.056 3520 Dihedral : 9.528 178.798 2811 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.95 % Favored : 96.01 % Rotamer: Outliers : 2.06 % Allowed : 15.99 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: 0.66 (0.17), residues: 2455 helix: 0.86 (0.15), residues: 1221 sheet: 0.91 (0.26), residues: 389 loop : -0.26 (0.23), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 51 TYR 0.006 0.001 TYR C 263 PHE 0.014 0.001 PHE E 44 TRP 0.006 0.001 TRP G 325 HIS 0.005 0.001 HIS I 57 Details of bonding type rmsd covalent geometry : bond 0.00308 (19871) covalent geometry : angle 0.63488 (26968) hydrogen bonds : bond 0.03404 ( 892) hydrogen bonds : angle 4.90530 ( 2508) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 377 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 MET cc_start: 0.7388 (mtp) cc_final: 0.7077 (mtp) REVERT: B 192 ILE cc_start: 0.8065 (mt) cc_final: 0.7862 (mp) REVERT: B 204 MET cc_start: 0.7640 (ttm) cc_final: 0.6981 (ptm) REVERT: B 259 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7756 (mt-10) REVERT: B 319 MET cc_start: 0.7506 (ttm) cc_final: 0.7274 (tpp) REVERT: C 32 VAL cc_start: 0.8160 (p) cc_final: 0.7915 (m) REVERT: C 49 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7671 (mtpt) REVERT: C 100 MET cc_start: 0.7800 (mtp) cc_final: 0.7581 (mtp) REVERT: C 124 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7651 (mt-10) REVERT: C 318 ARG cc_start: 0.7377 (mtt90) cc_final: 0.7032 (mmt180) REVERT: C 319 MET cc_start: 0.7326 (tpp) cc_final: 0.7060 (tpp) REVERT: D 130 MET cc_start: 0.5566 (tpp) cc_final: 0.5266 (tpp) REVERT: D 200 MET cc_start: 0.7077 (mtm) cc_final: 0.6794 (ttm) REVERT: D 266 ARG cc_start: 0.7262 (ttm-80) cc_final: 0.6971 (ttm-80) REVERT: D 318 ARG cc_start: 0.6311 (mmt90) cc_final: 0.6084 (mmt-90) REVERT: E 130 MET cc_start: 0.7165 (mmm) cc_final: 0.5233 (tmm) REVERT: E 133 TYR cc_start: 0.7825 (m-80) cc_final: 0.6998 (m-80) REVERT: E 146 ARG cc_start: 0.8131 (mtm180) cc_final: 0.7852 (mtm180) REVERT: E 284 ASP cc_start: 0.7235 (m-30) cc_final: 0.6906 (t0) REVERT: F 78 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7951 (mt-10) REVERT: G 172 ARG cc_start: 0.6931 (tmt-80) cc_final: 0.6613 (tmt-80) REVERT: G 203 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7163 (tm-30) REVERT: G 319 MET cc_start: 0.7024 (ppp) cc_final: 0.6461 (ppp) REVERT: H 100 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7686 (mtm) outliers start: 42 outliers final: 29 residues processed: 394 average time/residue: 0.7263 time to fit residues: 315.5141 Evaluate side-chains 407 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 375 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 264 MET Chi-restraints excluded: chain F residue 295 GLU Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain H residue 30 GLU Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain I residue 41 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 160 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 2 optimal weight: 0.5980 chunk 50 optimal weight: 0.0980 chunk 38 optimal weight: 0.6980 chunk 188 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 227 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 40 GLN ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN F 179 GLN F 255 ASN G 40 GLN I 116 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.172634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.143234 restraints weight = 25603.329| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.05 r_work: 0.3626 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19871 Z= 0.144 Angle : 0.648 12.037 26968 Z= 0.294 Chirality : 0.042 0.152 3068 Planarity : 0.005 0.056 3520 Dihedral : 9.538 179.671 2811 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.03 % Favored : 95.93 % Rotamer: Outliers : 2.35 % Allowed : 16.18 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: 0.63 (0.17), residues: 2455 helix: 0.84 (0.15), residues: 1223 sheet: 0.86 (0.26), residues: 389 loop : -0.27 (0.23), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 198 TYR 0.007 0.001 TYR F 31 PHE 0.015 0.001 PHE F 276 TRP 0.006 0.001 TRP F 325 HIS 0.012 0.001 HIS B 238 Details of bonding type rmsd covalent geometry : bond 0.00344 (19871) covalent geometry : angle 0.64789 (26968) hydrogen bonds : bond 0.03487 ( 892) hydrogen bonds : angle 4.90669 ( 2508) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 388 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 MET cc_start: 0.7408 (mtp) cc_final: 0.7101 (mtp) REVERT: B 204 MET cc_start: 0.7596 (ttm) cc_final: 0.6944 (ptm) REVERT: B 259 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7768 (mt-10) REVERT: B 319 MET cc_start: 0.7508 (ttm) cc_final: 0.7290 (tpp) REVERT: C 32 VAL cc_start: 0.8194 (p) cc_final: 0.7964 (m) REVERT: C 124 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7684 (mt-10) REVERT: C 318 ARG cc_start: 0.7346 (mtt90) cc_final: 0.7000 (mmt180) REVERT: C 319 MET cc_start: 0.7285 (tpp) cc_final: 0.7013 (tpp) REVERT: D 130 MET cc_start: 0.5505 (tpp) cc_final: 0.5219 (tpp) REVERT: D 231 ARG cc_start: 0.6323 (OUTLIER) cc_final: 0.5380 (ttp-170) REVERT: D 266 ARG cc_start: 0.7300 (ttm-80) cc_final: 0.7006 (ttm-80) REVERT: D 318 ARG cc_start: 0.6339 (mmt90) cc_final: 0.6110 (mmt-90) REVERT: E 130 MET cc_start: 0.7191 (mmm) cc_final: 0.5316 (tmm) REVERT: E 133 TYR cc_start: 0.7815 (m-80) cc_final: 0.7059 (m-80) REVERT: E 284 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6963 (t0) REVERT: E 299 ASP cc_start: 0.6783 (m-30) cc_final: 0.6555 (m-30) REVERT: E 321 THR cc_start: 0.8478 (t) cc_final: 0.8133 (p) REVERT: F 78 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7964 (mt-10) REVERT: F 90 VAL cc_start: 0.7507 (OUTLIER) cc_final: 0.7192 (m) REVERT: G 172 ARG cc_start: 0.6896 (tmt-80) cc_final: 0.6554 (tmt-80) REVERT: G 203 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7125 (tm-30) REVERT: G 319 MET cc_start: 0.7038 (ppp) cc_final: 0.6518 (ppp) REVERT: H 100 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7717 (mtm) REVERT: I 150 ILE cc_start: 0.8091 (pt) cc_final: 0.7541 (mt) outliers start: 48 outliers final: 27 residues processed: 410 average time/residue: 0.6631 time to fit residues: 300.8632 Evaluate side-chains 418 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 386 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 295 GLU Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain H residue 30 GLU Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain I residue 41 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 7 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 170 optimal weight: 0.5980 chunk 214 optimal weight: 0.3980 chunk 220 optimal weight: 0.0670 chunk 4 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 105 optimal weight: 8.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 40 GLN ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 GLN F 255 ASN G 40 GLN I 116 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.172632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.143362 restraints weight = 25710.736| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.06 r_work: 0.3629 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19871 Z= 0.129 Angle : 0.638 11.709 26968 Z= 0.290 Chirality : 0.041 0.151 3068 Planarity : 0.005 0.058 3520 Dihedral : 9.474 179.669 2811 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.79 % Favored : 96.17 % Rotamer: Outliers : 2.40 % Allowed : 16.67 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: 0.69 (0.17), residues: 2455 helix: 0.90 (0.15), residues: 1224 sheet: 0.83 (0.26), residues: 391 loop : -0.23 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 51 TYR 0.006 0.001 TYR F 31 PHE 0.015 0.001 PHE F 276 TRP 0.006 0.001 TRP G 325 HIS 0.020 0.001 HIS B 238 Details of bonding type rmsd covalent geometry : bond 0.00304 (19871) covalent geometry : angle 0.63827 (26968) hydrogen bonds : bond 0.03379 ( 892) hydrogen bonds : angle 4.84762 ( 2508) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 390 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 MET cc_start: 0.7385 (mtp) cc_final: 0.7072 (mtp) REVERT: B 204 MET cc_start: 0.7608 (ttm) cc_final: 0.6955 (ptm) REVERT: B 319 MET cc_start: 0.7533 (ttm) cc_final: 0.7331 (tpp) REVERT: C 32 VAL cc_start: 0.8181 (p) cc_final: 0.7959 (m) REVERT: C 49 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7643 (mtpt) REVERT: C 124 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7659 (mt-10) REVERT: C 173 ASP cc_start: 0.7143 (m-30) cc_final: 0.6917 (m-30) REVERT: C 318 ARG cc_start: 0.7339 (mtt90) cc_final: 0.7044 (mmt-90) REVERT: C 319 MET cc_start: 0.7221 (tpp) cc_final: 0.6947 (tpp) REVERT: D 130 MET cc_start: 0.5506 (tpp) cc_final: 0.5210 (tpp) REVERT: D 265 ASP cc_start: 0.7157 (m-30) cc_final: 0.6779 (m-30) REVERT: D 266 ARG cc_start: 0.7277 (ttm-80) cc_final: 0.6849 (ttm-80) REVERT: D 299 ASP cc_start: 0.6331 (m-30) cc_final: 0.6108 (m-30) REVERT: D 318 ARG cc_start: 0.6313 (mmt90) cc_final: 0.6042 (mmt-90) REVERT: E 130 MET cc_start: 0.7191 (mmm) cc_final: 0.5310 (tmm) REVERT: E 133 TYR cc_start: 0.7832 (m-80) cc_final: 0.7072 (m-80) REVERT: E 135 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6442 (tt) REVERT: E 299 ASP cc_start: 0.6766 (m-30) cc_final: 0.6540 (m-30) REVERT: E 321 THR cc_start: 0.8445 (t) cc_final: 0.8072 (p) REVERT: F 78 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7965 (mt-10) REVERT: F 90 VAL cc_start: 0.7490 (OUTLIER) cc_final: 0.7201 (m) REVERT: G 172 ARG cc_start: 0.6898 (tmt-80) cc_final: 0.6571 (tmt-80) REVERT: G 203 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7159 (tm-30) REVERT: G 319 MET cc_start: 0.6928 (ppp) cc_final: 0.6350 (ppp) REVERT: H 100 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7735 (mtp) REVERT: I 150 ILE cc_start: 0.8083 (pt) cc_final: 0.7534 (mt) outliers start: 49 outliers final: 29 residues processed: 406 average time/residue: 0.6573 time to fit residues: 295.3137 Evaluate side-chains 421 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 388 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 264 MET Chi-restraints excluded: chain F residue 295 GLU Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain H residue 30 GLU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain I residue 41 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 86 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 234 optimal weight: 7.9990 chunk 217 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 230 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 220 optimal weight: 0.5980 chunk 159 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN D 40 GLN ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 GLN F 255 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.173593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.144367 restraints weight = 25412.820| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.04 r_work: 0.3615 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19871 Z= 0.165 Angle : 0.672 12.325 26968 Z= 0.307 Chirality : 0.043 0.154 3068 Planarity : 0.005 0.057 3520 Dihedral : 9.431 178.035 2811 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.36 % Favored : 95.60 % Rotamer: Outliers : 2.21 % Allowed : 17.51 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.54 (0.17), residues: 2455 helix: 0.76 (0.15), residues: 1231 sheet: 0.80 (0.26), residues: 391 loop : -0.30 (0.23), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 51 TYR 0.007 0.001 TYR F 263 PHE 0.015 0.001 PHE E 44 TRP 0.006 0.001 TRP F 325 HIS 0.014 0.001 HIS B 238 Details of bonding type rmsd covalent geometry : bond 0.00402 (19871) covalent geometry : angle 0.67202 (26968) hydrogen bonds : bond 0.03656 ( 892) hydrogen bonds : angle 4.93912 ( 2508) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 391 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LEU cc_start: 0.6028 (OUTLIER) cc_final: 0.5644 (tp) REVERT: A 264 MET cc_start: 0.7419 (mtp) cc_final: 0.7089 (mtp) REVERT: B 204 MET cc_start: 0.7640 (ttm) cc_final: 0.6996 (ptm) REVERT: B 259 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7785 (mt-10) REVERT: B 319 MET cc_start: 0.7519 (ttm) cc_final: 0.7285 (tpp) REVERT: C 32 VAL cc_start: 0.8205 (p) cc_final: 0.7971 (m) REVERT: C 49 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7686 (mtpt) REVERT: C 124 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7701 (mt-10) REVERT: C 297 ILE cc_start: 0.7041 (OUTLIER) cc_final: 0.6769 (mt) REVERT: C 318 ARG cc_start: 0.7316 (mtt90) cc_final: 0.6998 (mmt-90) REVERT: C 319 MET cc_start: 0.7231 (tpp) cc_final: 0.6950 (tpp) REVERT: D 130 MET cc_start: 0.5546 (tpp) cc_final: 0.5267 (tpp) REVERT: D 265 ASP cc_start: 0.7113 (m-30) cc_final: 0.6719 (m-30) REVERT: D 299 ASP cc_start: 0.6346 (m-30) cc_final: 0.6141 (m-30) REVERT: E 130 MET cc_start: 0.7219 (mmm) cc_final: 0.5349 (tmm) REVERT: E 133 TYR cc_start: 0.7847 (m-80) cc_final: 0.7099 (m-80) REVERT: E 299 ASP cc_start: 0.6806 (m-30) cc_final: 0.6598 (m-30) REVERT: E 321 THR cc_start: 0.8466 (t) cc_final: 0.8080 (p) REVERT: F 78 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7930 (mt-10) REVERT: F 90 VAL cc_start: 0.7354 (OUTLIER) cc_final: 0.7151 (m) REVERT: G 124 GLU cc_start: 0.7968 (pt0) cc_final: 0.7700 (pt0) REVERT: G 172 ARG cc_start: 0.6925 (tmt-80) cc_final: 0.6223 (ttt-90) REVERT: G 203 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7134 (tm-30) REVERT: G 319 MET cc_start: 0.6953 (ppp) cc_final: 0.6388 (ppp) REVERT: H 100 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7655 (mtt) REVERT: I 150 ILE cc_start: 0.8135 (pt) cc_final: 0.7601 (mt) outliers start: 45 outliers final: 30 residues processed: 412 average time/residue: 0.6807 time to fit residues: 310.4685 Evaluate side-chains 422 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 386 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 295 GLU Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain H residue 30 GLU Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain I residue 41 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 168 optimal weight: 0.0980 chunk 221 optimal weight: 0.7980 chunk 51 optimal weight: 0.2980 chunk 236 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 40 GLN ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 GLN F 255 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.175383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.146400 restraints weight = 25527.124| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.08 r_work: 0.3609 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19871 Z= 0.138 Angle : 0.662 12.546 26968 Z= 0.302 Chirality : 0.042 0.152 3068 Planarity : 0.006 0.110 3520 Dihedral : 9.304 178.628 2811 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.15 % Favored : 95.80 % Rotamer: Outliers : 1.96 % Allowed : 17.85 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: 0.59 (0.17), residues: 2455 helix: 0.82 (0.15), residues: 1231 sheet: 0.78 (0.26), residues: 391 loop : -0.27 (0.23), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG E 51 TYR 0.007 0.001 TYR F 31 PHE 0.013 0.001 PHE E 44 TRP 0.006 0.001 TRP G 325 HIS 0.017 0.001 HIS B 238 Details of bonding type rmsd covalent geometry : bond 0.00330 (19871) covalent geometry : angle 0.66151 (26968) hydrogen bonds : bond 0.03506 ( 892) hydrogen bonds : angle 4.90374 ( 2508) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 390 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LEU cc_start: 0.6011 (OUTLIER) cc_final: 0.5648 (tp) REVERT: A 227 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7337 (tp) REVERT: A 264 MET cc_start: 0.7412 (mtp) cc_final: 0.7072 (mtp) REVERT: B 121 VAL cc_start: 0.8245 (OUTLIER) cc_final: 0.7968 (m) REVERT: B 204 MET cc_start: 0.7665 (ttm) cc_final: 0.7023 (ptm) REVERT: B 319 MET cc_start: 0.7545 (ttm) cc_final: 0.7291 (tpp) REVERT: C 32 VAL cc_start: 0.8196 (p) cc_final: 0.7968 (m) REVERT: C 49 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7703 (mtpt) REVERT: C 124 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7648 (mt-10) REVERT: C 297 ILE cc_start: 0.7076 (OUTLIER) cc_final: 0.6824 (mt) REVERT: C 318 ARG cc_start: 0.7274 (mtt90) cc_final: 0.6943 (mmt-90) REVERT: C 319 MET cc_start: 0.7214 (tpp) cc_final: 0.6943 (tpp) REVERT: D 130 MET cc_start: 0.5521 (tpp) cc_final: 0.5249 (tpp) REVERT: D 200 MET cc_start: 0.7248 (ttm) cc_final: 0.6976 (ttm) REVERT: D 265 ASP cc_start: 0.7102 (m-30) cc_final: 0.6682 (m-30) REVERT: D 299 ASP cc_start: 0.6333 (m-30) cc_final: 0.6125 (m-30) REVERT: E 130 MET cc_start: 0.7205 (mmm) cc_final: 0.5325 (tmm) REVERT: E 133 TYR cc_start: 0.7831 (m-80) cc_final: 0.7112 (m-80) REVERT: E 195 ARG cc_start: 0.7912 (ttp80) cc_final: 0.7636 (ttt90) REVERT: E 252 ASP cc_start: 0.7956 (m-30) cc_final: 0.7421 (m-30) REVERT: E 321 THR cc_start: 0.8448 (t) cc_final: 0.8049 (p) REVERT: F 78 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7910 (mt-10) REVERT: G 124 GLU cc_start: 0.7997 (pt0) cc_final: 0.7762 (pt0) REVERT: G 172 ARG cc_start: 0.6905 (tmt-80) cc_final: 0.6210 (ttt-90) REVERT: G 203 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7142 (tm-30) REVERT: G 319 MET cc_start: 0.6962 (ppp) cc_final: 0.6394 (ppp) REVERT: H 100 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7675 (mtm) REVERT: I 150 ILE cc_start: 0.8158 (pt) cc_final: 0.7642 (mt) outliers start: 40 outliers final: 32 residues processed: 405 average time/residue: 0.6516 time to fit residues: 291.8075 Evaluate side-chains 423 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 385 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain F residue 295 GLU Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain H residue 30 GLU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain I residue 41 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 5 optimal weight: 0.5980 chunk 181 optimal weight: 0.7980 chunk 222 optimal weight: 0.6980 chunk 30 optimal weight: 0.0170 chunk 98 optimal weight: 6.9990 chunk 203 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 243 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN D 40 GLN ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 GLN F 255 ASN G 40 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.171797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.142588 restraints weight = 25541.419| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.04 r_work: 0.3615 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19871 Z= 0.142 Angle : 0.668 13.441 26968 Z= 0.304 Chirality : 0.042 0.170 3068 Planarity : 0.006 0.090 3520 Dihedral : 9.197 178.477 2811 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.11 % Favored : 95.85 % Rotamer: Outliers : 2.06 % Allowed : 18.24 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: 0.57 (0.17), residues: 2455 helix: 0.80 (0.15), residues: 1231 sheet: 0.73 (0.26), residues: 389 loop : -0.27 (0.23), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 51 TYR 0.007 0.001 TYR F 31 PHE 0.014 0.001 PHE F 276 TRP 0.006 0.001 TRP G 325 HIS 0.017 0.001 HIS B 238 Details of bonding type rmsd covalent geometry : bond 0.00340 (19871) covalent geometry : angle 0.66753 (26968) hydrogen bonds : bond 0.03512 ( 892) hydrogen bonds : angle 4.91375 ( 2508) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8080.05 seconds wall clock time: 137 minutes 43.73 seconds (8263.73 seconds total)