Starting phenix.real_space_refine on Fri Jul 3 14:40:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uuu_64518/07_2026/9uuu_64518.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uuu_64518/07_2026/9uuu_64518.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uuu_64518/07_2026/9uuu_64518.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uuu_64518/07_2026/9uuu_64518.map" model { file = "/net/cci-nas-00/data/ceres_data/9uuu_64518/07_2026/9uuu_64518.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uuu_64518/07_2026/9uuu_64518.cif" } resolution = 3.17 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= 0.074 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 4 7.16 5 P 6 5.49 5 S 92 5.16 5 C 9490 2.51 5 N 2413 2.21 5 O 2688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14694 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3416 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 422} Chain: "B" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2933 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 14, 'TRANS': 368} Chain: "C" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1902 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain: "D" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1580 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "E" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1511 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "F" Number of atoms: 3157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3157 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 383} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'FMN': 1, 'RBF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 101 Unusual residues: {'FAD': 1, 'FES': 1, 'NAI': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8436 SG CYS D 29 48.369 58.911 63.309 1.00 82.13 S Time building chain proxies: 2.74, per 1000 atoms: 0.19 Number of scatterers: 14694 At special positions: 0 Unit cell: (91.52, 126.72, 154.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 Ca 1 19.99 S 92 16.00 P 6 15.00 O 2688 8.00 N 2413 7.00 C 9490 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 525.8 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D 301 " pdb="FE2 FES D 301 " - pdb=" SG CYS D 29 " pdb="FE2 FES D 301 " - pdb=" SG CYS E 120 " pdb="FE1 FES D 301 " - pdb=" SG CYS E 26 " Number of angles added : 4 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3416 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 14 sheets defined 50.4% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 107 through 113 removed outlier: 3.706A pdb=" N LEU A 110 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA A 111 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER A 112 " --> pdb=" O GLN A 109 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 113 " --> pdb=" O LEU A 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 107 through 113' Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 162 through 168 removed outlier: 3.771A pdb=" N VAL A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 219 through 228 Processing helix chain 'A' and resid 241 through 254 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 310 through 314 removed outlier: 3.897A pdb=" N HIS A 313 " --> pdb=" O THR A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 339 removed outlier: 3.647A pdb=" N MET A 339 " --> pdb=" O GLY A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.801A pdb=" N HIS A 354 " --> pdb=" O PHE A 351 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 355 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 384 removed outlier: 3.735A pdb=" N VAL A 383 " --> pdb=" O ASN A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 401 through 409 Processing helix chain 'A' and resid 418 through 424 Processing helix chain 'A' and resid 430 through 446 removed outlier: 3.930A pdb=" N LEU A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.936A pdb=" N VAL B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 87 Processing helix chain 'B' and resid 89 through 97 Processing helix chain 'B' and resid 99 through 108 removed outlier: 3.773A pdb=" N THR B 105 " --> pdb=" O HIS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 151 removed outlier: 3.674A pdb=" N TYR B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 158 through 168 removed outlier: 3.751A pdb=" N ILE B 164 " --> pdb=" O PHE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.567A pdb=" N GLY B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 245 removed outlier: 3.556A pdb=" N TRP B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 249 removed outlier: 3.771A pdb=" N LEU B 249 " --> pdb=" O ALA B 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 246 through 249' Processing helix chain 'B' and resid 259 through 266 Processing helix chain 'B' and resid 276 through 290 removed outlier: 4.251A pdb=" N PHE B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE B 287 " --> pdb=" O GLY B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 316 Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 353 through 375 removed outlier: 3.906A pdb=" N TRP B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN B 375 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 410 removed outlier: 4.580A pdb=" N LEU B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Proline residue: B 394 - end of helix Processing helix chain 'C' and resid 7 through 32 Processing helix chain 'C' and resid 33 through 53 removed outlier: 4.131A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 70 removed outlier: 3.501A pdb=" N LYS C 69 " --> pdb=" O GLU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 177 through 181 removed outlier: 3.937A pdb=" N VAL C 180 " --> pdb=" O GLY C 177 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU C 181 " --> pdb=" O GLY C 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 181' Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 224 through 239 removed outlier: 3.742A pdb=" N GLY C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE C 235 " --> pdb=" O VAL C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 254 Processing helix chain 'D' and resid 6 through 13 Processing helix chain 'D' and resid 28 through 35 removed outlier: 4.204A pdb=" N THR D 35 " --> pdb=" O ALA D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 62 Processing helix chain 'D' and resid 70 through 94 Processing helix chain 'D' and resid 94 through 101 Processing helix chain 'D' and resid 111 through 121 removed outlier: 4.034A pdb=" N MET D 115 " --> pdb=" O ASN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 158 removed outlier: 4.140A pdb=" N VAL D 144 " --> pdb=" O GLY D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 202 removed outlier: 3.975A pdb=" N ALA D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 206 removed outlier: 4.008A pdb=" N VAL D 206 " --> pdb=" O PRO D 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 203 through 206' Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 24 through 31 Processing helix chain 'E' and resid 34 through 63 Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 78 through 101 removed outlier: 4.409A pdb=" N PHE E 101 " --> pdb=" O ILE E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 117 removed outlier: 3.886A pdb=" N PHE E 112 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU E 113 " --> pdb=" O GLY E 110 " (cutoff:3.500A) Proline residue: E 114 - end of helix removed outlier: 3.727A pdb=" N THR E 117 " --> pdb=" O PRO E 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 109 through 117' Processing helix chain 'E' and resid 119 through 133 removed outlier: 3.951A pdb=" N PHE E 123 " --> pdb=" O ASN E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 164 Processing helix chain 'E' and resid 170 through 174 Processing helix chain 'E' and resid 175 through 190 Processing helix chain 'E' and resid 191 through 194 removed outlier: 3.525A pdb=" N SER E 194 " --> pdb=" O MET E 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 191 through 194' Processing helix chain 'F' and resid 2 through 30 removed outlier: 3.572A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 42 Processing helix chain 'F' and resid 55 through 63 removed outlier: 3.800A pdb=" N LEU F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 98 Processing helix chain 'F' and resid 99 through 104 Processing helix chain 'F' and resid 178 through 182 Processing helix chain 'F' and resid 187 through 195 removed outlier: 4.351A pdb=" N ASP F 191 " --> pdb=" O LYS F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 200 removed outlier: 3.981A pdb=" N TYR F 200 " --> pdb=" O LEU F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 251 removed outlier: 4.095A pdb=" N SER F 251 " --> pdb=" O SER F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 298 removed outlier: 4.417A pdb=" N MET F 288 " --> pdb=" O GLY F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 330 removed outlier: 3.970A pdb=" N PHE F 323 " --> pdb=" O TYR F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 347 removed outlier: 3.736A pdb=" N ASP F 346 " --> pdb=" O GLN F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 363 removed outlier: 3.548A pdb=" N TYR F 360 " --> pdb=" O HIS F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 373 Processing helix chain 'F' and resid 381 through 393 removed outlier: 4.665A pdb=" N VAL F 387 " --> pdb=" O MET F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 399 No H-bonds generated for 'chain 'F' and resid 397 through 399' Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 6.889A pdb=" N ILE A 149 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N CYS A 192 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A 151 " --> pdb=" O CYS A 192 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA A 148 " --> pdb=" O TRP A 237 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ILE A 239 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE A 150 " --> pdb=" O ILE A 239 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 21 removed outlier: 5.937A pdb=" N GLN A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR A 307 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 30 removed outlier: 6.830A pdb=" N LEU A 87 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG A 81 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N SER A 89 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ILE A 79 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL A 91 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 43 removed outlier: 3.678A pdb=" N THR A 42 " --> pdb=" O GLU A 59 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 71 through 77 removed outlier: 3.738A pdb=" N VAL C 124 " --> pdb=" O ARG C 74 " (cutoff:3.500A) removed outlier: 15.566A pdb=" N VAL C 121 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 11.887A pdb=" N VAL C 140 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N VAL C 123 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU C 138 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR C 125 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL C 136 " --> pdb=" O TYR C 125 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL C 127 " --> pdb=" O SER C 134 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N MET C 148 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLU C 169 " --> pdb=" O MET C 148 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N TYR C 150 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N TYR C 167 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N PHE C 152 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LEU C 165 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA C 154 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 103 through 105 removed outlier: 3.643A pdb=" N ARG C 118 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 204 through 206 removed outlier: 6.701A pdb=" N LYS C 204 " --> pdb=" O VAL C 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AA9, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AB1, first strand: chain 'F' and resid 80 through 81 Processing sheet with id=AB2, first strand: chain 'F' and resid 151 through 153 removed outlier: 7.342A pdb=" N LYS F 151 " --> pdb=" O ILE F 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 148 through 149 Processing sheet with id=AB4, first strand: chain 'F' and resid 276 through 279 removed outlier: 6.402A pdb=" N TYR F 375 " --> pdb=" O LEU F 402 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 307 through 311 removed outlier: 3.591A pdb=" N HIS F 336 " --> pdb=" O TYR F 307 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA F 338 " --> pdb=" O TYR F 309 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR F 351 " --> pdb=" O CYS F 337 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU F 339 " --> pdb=" O TYR F 351 " (cutoff:3.500A) 671 hydrogen bonds defined for protein. 1938 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.85 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.38: 5632 1.38 - 1.58: 9231 1.58 - 1.79: 77 1.79 - 1.99: 87 1.99 - 2.20: 8 Bond restraints: 15035 Sorted by residual: bond pdb=" C2B NAI F 503 " pdb=" C3B NAI F 503 " ideal model delta sigma weight residual 1.530 1.236 0.294 2.00e-02 2.50e+03 2.16e+02 bond pdb=" C3D NAI F 503 " pdb=" C4D NAI F 503 " ideal model delta sigma weight residual 1.524 1.274 0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" C1D NAI F 503 " pdb=" C2D NAI F 503 " ideal model delta sigma weight residual 1.528 1.278 0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" C5N NAI F 503 " pdb=" C6N NAI F 503 " ideal model delta sigma weight residual 1.330 1.531 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C2N NAI F 503 " pdb=" C3N NAI F 503 " ideal model delta sigma weight residual 1.348 1.523 -0.175 2.00e-02 2.50e+03 7.62e+01 ... (remaining 15030 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.06: 20266 4.06 - 8.12: 126 8.12 - 12.18: 12 12.18 - 16.24: 11 16.24 - 20.30: 3 Bond angle restraints: 20418 Sorted by residual: angle pdb=" S1 FES D 301 " pdb="FE2 FES D 301 " pdb=" S2 FES D 301 " ideal model delta sigma weight residual 104.33 90.56 13.77 1.14e+00 7.69e-01 1.46e+02 angle pdb="FE1 FES D 301 " pdb=" S2 FES D 301 " pdb="FE2 FES D 301 " ideal model delta sigma weight residual 75.66 89.12 -13.46 1.14e+00 7.69e-01 1.39e+02 angle pdb=" S1 FES D 301 " pdb="FE1 FES D 301 " pdb=" S2 FES D 301 " ideal model delta sigma weight residual 104.33 90.36 13.97 1.20e+00 6.94e-01 1.36e+02 angle pdb=" S1 FES F 501 " pdb="FE2 FES F 501 " pdb=" S2 FES F 501 " ideal model delta sigma weight residual 104.33 91.15 13.18 1.14e+00 7.69e-01 1.34e+02 angle pdb="FE1 FES F 501 " pdb=" S2 FES F 501 " pdb="FE2 FES F 501 " ideal model delta sigma weight residual 75.66 88.77 -13.11 1.14e+00 7.69e-01 1.32e+02 ... (remaining 20413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.00: 8071 20.00 - 39.99: 660 39.99 - 59.99: 116 59.99 - 79.99: 23 79.99 - 99.98: 10 Dihedral angle restraints: 8880 sinusoidal: 3525 harmonic: 5355 Sorted by residual: dihedral pdb=" CA VAL F 66 " pdb=" C VAL F 66 " pdb=" N SER F 67 " pdb=" CA SER F 67 " ideal model delta harmonic sigma weight residual -180.00 -132.29 -47.71 0 5.00e+00 4.00e-02 9.10e+01 dihedral pdb=" CA ARG B 43 " pdb=" C ARG B 43 " pdb=" N SER B 44 " pdb=" CA SER B 44 " ideal model delta harmonic sigma weight residual -180.00 -150.24 -29.76 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA PHE F 65 " pdb=" C PHE F 65 " pdb=" N VAL F 66 " pdb=" CA VAL F 66 " ideal model delta harmonic sigma weight residual 180.00 150.91 29.09 0 5.00e+00 4.00e-02 3.39e+01 ... (remaining 8877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1893 0.067 - 0.133: 373 0.133 - 0.199: 36 0.199 - 0.266: 2 0.266 - 0.332: 2 Chirality restraints: 2306 Sorted by residual: chirality pdb=" C3B NAI F 503 " pdb=" C2B NAI F 503 " pdb=" C4B NAI F 503 " pdb=" O3B NAI F 503 " both_signs ideal model delta sigma weight residual False -2.72 -2.38 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" C3D NAI F 503 " pdb=" C2D NAI F 503 " pdb=" C4D NAI F 503 " pdb=" O3D NAI F 503 " both_signs ideal model delta sigma weight residual False -2.71 -2.42 -0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C4' RBF B 502 " pdb=" C3' RBF B 502 " pdb=" C5' RBF B 502 " pdb=" O4' RBF B 502 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 2303 not shown) Planarity restraints: 2567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 66 " -0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C VAL F 66 " 0.064 2.00e-02 2.50e+03 pdb=" O VAL F 66 " -0.024 2.00e-02 2.50e+03 pdb=" N SER F 67 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO E 103 " 0.060 5.00e-02 4.00e+02 9.04e-02 1.31e+01 pdb=" N PRO E 104 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO E 104 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO E 104 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 286 " -0.049 5.00e-02 4.00e+02 7.41e-02 8.78e+00 pdb=" N PRO F 287 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO F 287 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO F 287 " -0.041 5.00e-02 4.00e+02 ... (remaining 2564 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3578 2.79 - 3.31: 13258 3.31 - 3.84: 23747 3.84 - 4.37: 27447 4.37 - 4.90: 48754 Nonbonded interactions: 116784 Sorted by model distance: nonbonded pdb=" OD1 ASP A 179 " pdb=" OG SER A 201 " model vdw 2.257 3.040 nonbonded pdb=" O GLN A 249 " pdb=" OG1 THR A 253 " model vdw 2.260 3.040 nonbonded pdb=" O PHE E 28 " pdb=" OG SER E 32 " model vdw 2.263 3.040 nonbonded pdb=" NE1 TRP B 260 " pdb=" O HIS B 328 " model vdw 2.265 3.120 nonbonded pdb=" OG1 THR B 236 " pdb=" O3P FMN B 501 " model vdw 2.278 3.040 ... (remaining 116779 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.090 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 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 : 0.014 0.737 15038 Z= 0.507 Angle : 1.054 26.611 20422 Z= 0.568 Chirality : 0.053 0.332 2306 Planarity : 0.007 0.090 2567 Dihedral : 15.329 99.983 5464 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.59 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.13 (0.16), residues: 1880 helix: -1.39 (0.15), residues: 844 sheet: -3.16 (0.36), residues: 142 loop : -2.56 (0.16), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 209 TYR 0.021 0.002 TYR F 307 PHE 0.042 0.002 PHE B 323 TRP 0.030 0.002 TRP B 103 HIS 0.005 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00983 / 0.45 (15035) covalent geometry : angle 1.01843 / 0.57 (20418) hydrogen bonds : bond 0.13329 / 9.08 ( 671) hydrogen bonds : angle 6.21891 / 4.29 ( 1938) metal coordination : bond 0.70344 / 35.15 ( 3) metal coordination : angle 19.49890 / 8.76 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.351 Fit side-chains REVERT: A 5 LYS cc_start: 0.8520 (mttp) cc_final: 0.7965 (mttm) REVERT: A 22 ASP cc_start: 0.7603 (t0) cc_final: 0.7361 (t0) REVERT: B 42 LYS cc_start: 0.8139 (mmtt) cc_final: 0.7666 (mtmm) REVERT: B 151 ARG cc_start: 0.5517 (mmm160) cc_final: 0.4355 (ptp-110) REVERT: B 152 LYS cc_start: 0.8935 (ttmt) cc_final: 0.8083 (tppt) REVERT: B 156 ASN cc_start: 0.8074 (p0) cc_final: 0.7760 (p0) REVERT: B 302 MET cc_start: 0.8069 (tpp) cc_final: 0.7859 (tpt) REVERT: B 367 MET cc_start: 0.8465 (mmm) cc_final: 0.8041 (mmt) REVERT: C 51 GLN cc_start: 0.8147 (tm-30) cc_final: 0.7833 (tm-30) REVERT: D 18 ASN cc_start: 0.8149 (t0) cc_final: 0.7546 (t0) REVERT: D 119 GLU cc_start: 0.8596 (tp30) cc_final: 0.8304 (tp30) REVERT: D 139 LEU cc_start: 0.7751 (mt) cc_final: 0.7478 (mp) REVERT: E 15 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7837 (mt-10) REVERT: E 73 VAL cc_start: 0.8982 (t) cc_final: 0.8704 (p) REVERT: F 10 MET cc_start: 0.8211 (mmm) cc_final: 0.7891 (mmt) REVERT: F 276 MET cc_start: 0.7799 (mtt) cc_final: 0.7437 (mtp) REVERT: F 285 MET cc_start: 0.6171 (tmm) cc_final: 0.5856 (tmm) REVERT: F 319 TYR cc_start: 0.7092 (m-10) cc_final: 0.6667 (m-10) REVERT: F 336 HIS cc_start: 0.8346 (m-70) cc_final: 0.7758 (m-70) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.1207 time to fit residues: 36.1239 Evaluate side-chains 160 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 HIS A 242 GLN A 343 ASN B 84 ASN B 243 GLN B 313 ASN C 110 GLN D 68 ASN D 171 ASN F 40 ASN ** F 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 ASN ** F 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.161774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.108370 restraints weight = 18741.217| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.93 r_work: 0.3090 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15038 Z= 0.190 Angle : 0.613 10.709 20422 Z= 0.320 Chirality : 0.044 0.154 2306 Planarity : 0.006 0.078 2567 Dihedral : 8.795 81.430 2151 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.64 % Favored : 94.31 % Rotamer: Outliers : 1.23 % Allowed : 10.63 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.18), residues: 1880 helix: 0.11 (0.18), residues: 845 sheet: -2.89 (0.37), residues: 151 loop : -2.07 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 118 TYR 0.018 0.001 TYR B 360 PHE 0.028 0.002 PHE D 50 TRP 0.024 0.002 TRP B 103 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (15035) covalent geometry : angle 0.61078 / 0.32 (20418) hydrogen bonds : bond 0.05176 / 3.40 ( 671) hydrogen bonds : angle 4.98451 / 3.37 ( 1938) metal coordination : bond 0.02016 / 1.02 ( 3) metal coordination : angle 3.72129 / 2.08 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8764 (mttp) cc_final: 0.8196 (mttm) REVERT: B 42 LYS cc_start: 0.8391 (mmtt) cc_final: 0.7913 (mtmm) REVERT: B 151 ARG cc_start: 0.5622 (mmm160) cc_final: 0.4524 (ptp-110) REVERT: B 152 LYS cc_start: 0.8972 (ttmt) cc_final: 0.8165 (tppt) REVERT: B 322 MET cc_start: 0.9088 (mmm) cc_final: 0.8856 (mtp) REVERT: B 367 MET cc_start: 0.8824 (mmm) cc_final: 0.8504 (mmt) REVERT: C 51 GLN cc_start: 0.8404 (tm-30) cc_final: 0.8127 (tm-30) REVERT: C 74 ARG cc_start: 0.7517 (mmt180) cc_final: 0.7143 (mtt-85) REVERT: D 44 MET cc_start: 0.9012 (tpt) cc_final: 0.8220 (tpt) REVERT: D 119 GLU cc_start: 0.8833 (tp30) cc_final: 0.8574 (tp30) REVERT: D 139 LEU cc_start: 0.7915 (mt) cc_final: 0.7680 (mp) REVERT: E 73 VAL cc_start: 0.9009 (t) cc_final: 0.8719 (p) REVERT: F 119 MET cc_start: 0.4622 (OUTLIER) cc_final: 0.4354 (tpp) REVERT: F 276 MET cc_start: 0.8032 (mtt) cc_final: 0.7513 (mtp) REVERT: F 285 MET cc_start: 0.6343 (tmm) cc_final: 0.5992 (tmm) REVERT: F 319 TYR cc_start: 0.7425 (m-10) cc_final: 0.7091 (m-10) outliers start: 19 outliers final: 13 residues processed: 180 average time/residue: 0.1078 time to fit residues: 29.4670 Evaluate side-chains 167 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain C residue 110 GLN Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 356 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 12 optimal weight: 1.9990 chunk 144 optimal weight: 0.0060 chunk 103 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 60 optimal weight: 0.5980 chunk 174 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 99 optimal weight: 0.0980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 243 GLN D 68 ASN F 216 ASN F 244 GLN ** F 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.167395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.115383 restraints weight = 18809.975| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.43 r_work: 0.3181 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 15038 Z= 0.105 Angle : 0.527 11.028 20422 Z= 0.275 Chirality : 0.041 0.147 2306 Planarity : 0.005 0.072 2567 Dihedral : 7.834 77.329 2151 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.36 % Allowed : 11.47 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.89 (0.19), residues: 1880 helix: 0.97 (0.18), residues: 836 sheet: -2.55 (0.37), residues: 146 loop : -1.81 (0.19), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 118 TYR 0.014 0.001 TYR D 141 PHE 0.025 0.001 PHE D 50 TRP 0.023 0.001 TRP B 103 HIS 0.005 0.001 HIS F 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (15035) covalent geometry : angle 0.52570 / 0.28 (20418) hydrogen bonds : bond 0.04005 / 2.61 ( 671) hydrogen bonds : angle 4.52829 / 3.07 ( 1938) metal coordination : bond 0.00147 / 0.08 ( 3) metal coordination : angle 3.12706 / 1.80 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 0.553 Fit side-chains REVERT: A 5 LYS cc_start: 0.8846 (mttp) cc_final: 0.8267 (mttm) REVERT: B 151 ARG cc_start: 0.5674 (mmm160) cc_final: 0.4824 (ptp-110) REVERT: B 152 LYS cc_start: 0.9025 (ttmt) cc_final: 0.8270 (tppt) REVERT: B 322 MET cc_start: 0.8953 (mmm) cc_final: 0.8715 (mtp) REVERT: C 51 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8199 (tm-30) REVERT: C 74 ARG cc_start: 0.7475 (mmt180) cc_final: 0.7147 (mtt-85) REVERT: C 141 HIS cc_start: 0.8676 (p90) cc_final: 0.8463 (p-80) REVERT: D 18 ASN cc_start: 0.8447 (t0) cc_final: 0.7958 (t0) REVERT: D 119 GLU cc_start: 0.8834 (tp30) cc_final: 0.8607 (tp30) REVERT: D 139 LEU cc_start: 0.8016 (mt) cc_final: 0.7809 (mp) REVERT: E 17 MET cc_start: 0.8247 (mmm) cc_final: 0.7990 (mmt) REVERT: F 119 MET cc_start: 0.4807 (OUTLIER) cc_final: 0.4540 (tpp) REVERT: F 276 MET cc_start: 0.8082 (mtt) cc_final: 0.7806 (mtp) REVERT: F 285 MET cc_start: 0.6291 (tmm) cc_final: 0.5976 (tmm) REVERT: F 293 PHE cc_start: 0.7844 (OUTLIER) cc_final: 0.7397 (m-80) REVERT: F 319 TYR cc_start: 0.7308 (m-10) cc_final: 0.7103 (m-80) REVERT: F 336 HIS cc_start: 0.7991 (m-70) cc_final: 0.7622 (m-70) outliers start: 21 outliers final: 13 residues processed: 197 average time/residue: 0.1072 time to fit residues: 32.1336 Evaluate side-chains 175 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 293 PHE Chi-restraints excluded: chain F residue 356 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 13 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 167 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 172 optimal weight: 8.9990 chunk 56 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 GLN B 243 GLN D 68 ASN ** F 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.160577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.107060 restraints weight = 18829.542| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.74 r_work: 0.3079 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15038 Z= 0.196 Angle : 0.578 11.915 20422 Z= 0.299 Chirality : 0.044 0.152 2306 Planarity : 0.005 0.065 2567 Dihedral : 7.734 73.195 2151 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.59 % Allowed : 13.16 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.85 (0.19), residues: 1880 helix: 0.94 (0.18), residues: 844 sheet: -2.60 (0.35), residues: 165 loop : -1.68 (0.20), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 104 TYR 0.018 0.001 TYR B 360 PHE 0.023 0.001 PHE D 50 TRP 0.025 0.002 TRP B 103 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 (15035) covalent geometry : angle 0.57570 / 0.30 (20418) hydrogen bonds : bond 0.04786 / 3.13 ( 671) hydrogen bonds : angle 4.56376 / 3.09 ( 1938) metal coordination : bond 0.01453 / 0.73 ( 3) metal coordination : angle 3.50741 / 1.98 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 157 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8742 (mttp) cc_final: 0.8096 (mttm) REVERT: B 42 LYS cc_start: 0.8270 (mmtt) cc_final: 0.7780 (mtmm) REVERT: B 151 ARG cc_start: 0.5512 (mmm160) cc_final: 0.4376 (ptp-110) REVERT: B 152 LYS cc_start: 0.8833 (ttmt) cc_final: 0.8001 (tppt) REVERT: B 322 MET cc_start: 0.9007 (mmm) cc_final: 0.8805 (mtp) REVERT: C 51 GLN cc_start: 0.8330 (tm-30) cc_final: 0.8054 (tm-30) REVERT: D 119 GLU cc_start: 0.8770 (tp30) cc_final: 0.8466 (tp30) REVERT: D 139 LEU cc_start: 0.7675 (mt) cc_final: 0.7445 (mp) REVERT: E 1 MET cc_start: 0.6179 (mmt) cc_final: 0.5274 (ptm) REVERT: E 17 MET cc_start: 0.8248 (mmm) cc_final: 0.7956 (mmt) REVERT: E 51 ILE cc_start: 0.8230 (mm) cc_final: 0.7769 (tp) REVERT: F 119 MET cc_start: 0.4429 (OUTLIER) cc_final: 0.4209 (tpp) REVERT: F 123 LEU cc_start: 0.4227 (OUTLIER) cc_final: 0.3944 (tt) REVERT: F 285 MET cc_start: 0.6224 (tmm) cc_final: 0.5860 (tmm) REVERT: F 293 PHE cc_start: 0.7791 (OUTLIER) cc_final: 0.7433 (m-80) REVERT: F 308 TRP cc_start: 0.7384 (m100) cc_final: 0.7141 (m100) REVERT: F 319 TYR cc_start: 0.7198 (m-10) cc_final: 0.6951 (m-80) outliers start: 40 outliers final: 24 residues processed: 185 average time/residue: 0.1074 time to fit residues: 30.3021 Evaluate side-chains 180 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 181 ASP Chi-restraints excluded: chain F residue 200 TYR Chi-restraints excluded: chain F residue 293 PHE Chi-restraints excluded: chain F residue 356 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 91 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 243 GLN D 68 ASN ** F 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.163483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.110638 restraints weight = 18619.255| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.03 r_work: 0.3107 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15038 Z= 0.142 Angle : 0.532 11.519 20422 Z= 0.276 Chirality : 0.042 0.149 2306 Planarity : 0.005 0.063 2567 Dihedral : 7.528 72.087 2151 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.20 % Allowed : 14.19 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.19), residues: 1880 helix: 1.18 (0.18), residues: 846 sheet: -2.39 (0.36), residues: 163 loop : -1.53 (0.20), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 104 TYR 0.015 0.001 TYR B 360 PHE 0.027 0.001 PHE F 182 TRP 0.030 0.002 TRP F 250 HIS 0.003 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (15035) covalent geometry : angle 0.52935 / 0.28 (20418) hydrogen bonds : bond 0.04281 / 2.79 ( 671) hydrogen bonds : angle 4.42125 / 2.99 ( 1938) metal coordination : bond 0.00974 / 0.49 ( 3) metal coordination : angle 3.49570 / 1.99 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8764 (mttp) cc_final: 0.8130 (mttm) REVERT: B 151 ARG cc_start: 0.5516 (mmm160) cc_final: 0.4465 (ptp-110) REVERT: B 152 LYS cc_start: 0.8892 (ttmt) cc_final: 0.8086 (tppt) REVERT: B 322 MET cc_start: 0.9033 (mmm) cc_final: 0.8810 (mtp) REVERT: C 51 GLN cc_start: 0.8377 (tm-30) cc_final: 0.8113 (tm-30) REVERT: D 18 ASN cc_start: 0.8335 (t0) cc_final: 0.7822 (t0) REVERT: D 119 GLU cc_start: 0.8789 (tp30) cc_final: 0.8502 (tp30) REVERT: D 139 LEU cc_start: 0.7720 (mt) cc_final: 0.7503 (mp) REVERT: E 1 MET cc_start: 0.6099 (mmt) cc_final: 0.5142 (ptm) REVERT: E 17 MET cc_start: 0.8259 (mmm) cc_final: 0.7997 (mmt) REVERT: E 48 VAL cc_start: 0.7823 (t) cc_final: 0.7441 (t) REVERT: E 51 ILE cc_start: 0.8355 (mm) cc_final: 0.7964 (tp) REVERT: F 123 LEU cc_start: 0.4246 (OUTLIER) cc_final: 0.3948 (tt) REVERT: F 214 MET cc_start: 0.5932 (mpp) cc_final: 0.5623 (mpp) REVERT: F 285 MET cc_start: 0.6187 (tmm) cc_final: 0.5848 (tmm) REVERT: F 293 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7452 (m-80) REVERT: F 308 TRP cc_start: 0.7721 (m100) cc_final: 0.7511 (m100) REVERT: F 319 TYR cc_start: 0.7143 (m-10) cc_final: 0.6883 (m-80) REVERT: F 336 HIS cc_start: 0.7953 (m90) cc_final: 0.7205 (m90) outliers start: 34 outliers final: 22 residues processed: 190 average time/residue: 0.1010 time to fit residues: 29.5859 Evaluate side-chains 178 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 181 ASP Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 293 PHE Chi-restraints excluded: chain F residue 356 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 41 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 174 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 GLN B 243 GLN C 110 GLN D 68 ASN ** F 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.162478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.109510 restraints weight = 18868.275| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.87 r_work: 0.3107 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15038 Z= 0.167 Angle : 0.550 11.709 20422 Z= 0.284 Chirality : 0.043 0.150 2306 Planarity : 0.005 0.062 2567 Dihedral : 7.462 70.182 2151 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.33 % Allowed : 14.32 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.19), residues: 1880 helix: 1.18 (0.18), residues: 846 sheet: -2.27 (0.37), residues: 162 loop : -1.50 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 118 TYR 0.016 0.001 TYR B 360 PHE 0.026 0.001 PHE F 182 TRP 0.031 0.002 TRP F 250 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (15035) covalent geometry : angle 0.54774 / 0.28 (20418) hydrogen bonds : bond 0.04498 / 2.93 ( 671) hydrogen bonds : angle 4.41703 / 2.99 ( 1938) metal coordination : bond 0.01276 / 0.64 ( 3) metal coordination : angle 3.59608 / 2.00 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 0.577 Fit side-chains REVERT: A 5 LYS cc_start: 0.8814 (mttp) cc_final: 0.8192 (mttm) REVERT: B 151 ARG cc_start: 0.5555 (mmm160) cc_final: 0.4520 (ptp-110) REVERT: B 152 LYS cc_start: 0.8918 (ttmt) cc_final: 0.8125 (tppt) REVERT: B 322 MET cc_start: 0.9021 (mmm) cc_final: 0.8812 (mtp) REVERT: C 51 GLN cc_start: 0.8412 (tm-30) cc_final: 0.8131 (tm-30) REVERT: C 74 ARG cc_start: 0.7287 (mmt180) cc_final: 0.6981 (mtt-85) REVERT: D 119 GLU cc_start: 0.8790 (tp30) cc_final: 0.8500 (tp30) REVERT: D 139 LEU cc_start: 0.7838 (mt) cc_final: 0.7602 (mp) REVERT: E 1 MET cc_start: 0.6106 (mmt) cc_final: 0.5212 (ptm) REVERT: E 17 MET cc_start: 0.8308 (mmm) cc_final: 0.8042 (mmt) REVERT: E 51 ILE cc_start: 0.8452 (mm) cc_final: 0.8057 (tp) REVERT: F 123 LEU cc_start: 0.4147 (OUTLIER) cc_final: 0.3851 (tt) REVERT: F 285 MET cc_start: 0.6219 (tmm) cc_final: 0.5905 (tmm) REVERT: F 293 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.7422 (m-80) REVERT: F 308 TRP cc_start: 0.7819 (m100) cc_final: 0.7614 (m100) REVERT: F 319 TYR cc_start: 0.7229 (m-10) cc_final: 0.6969 (m-80) REVERT: F 336 HIS cc_start: 0.8002 (m90) cc_final: 0.7138 (m90) outliers start: 36 outliers final: 24 residues processed: 187 average time/residue: 0.1080 time to fit residues: 31.4485 Evaluate side-chains 182 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 293 PHE Chi-restraints excluded: chain F residue 356 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 48 optimal weight: 2.9990 chunk 73 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 171 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 138 optimal weight: 0.4980 chunk 173 optimal weight: 9.9990 chunk 166 optimal weight: 30.0000 chunk 112 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 HIS B 243 GLN D 68 ASN F 384 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.166698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.114393 restraints weight = 18584.800| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.86 r_work: 0.3183 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15038 Z= 0.102 Angle : 0.517 14.657 20422 Z= 0.263 Chirality : 0.041 0.145 2306 Planarity : 0.004 0.060 2567 Dihedral : 7.226 70.944 2151 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.14 % Allowed : 15.29 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.20 (0.20), residues: 1880 helix: 1.50 (0.19), residues: 846 sheet: -2.08 (0.39), residues: 156 loop : -1.44 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 408 TYR 0.013 0.001 TYR D 141 PHE 0.021 0.001 PHE D 50 TRP 0.037 0.002 TRP F 250 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (15035) covalent geometry : angle 0.51518 / 0.26 (20418) hydrogen bonds : bond 0.03783 / 2.46 ( 671) hydrogen bonds : angle 4.24634 / 2.88 ( 1938) metal coordination : bond 0.00474 / 0.24 ( 3) metal coordination : angle 2.78421 / 1.59 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8865 (mttp) cc_final: 0.8215 (mttm) REVERT: B 151 ARG cc_start: 0.5443 (mmm160) cc_final: 0.4536 (ptp-110) REVERT: B 152 LYS cc_start: 0.8939 (ttmt) cc_final: 0.8174 (tppt) REVERT: C 51 GLN cc_start: 0.8430 (tm-30) cc_final: 0.8164 (tm-30) REVERT: C 74 ARG cc_start: 0.7262 (mmt180) cc_final: 0.6939 (mtt-85) REVERT: C 141 HIS cc_start: 0.8587 (p90) cc_final: 0.8327 (p-80) REVERT: D 18 ASN cc_start: 0.8402 (t0) cc_final: 0.7907 (t0) REVERT: D 50 PHE cc_start: 0.7710 (t80) cc_final: 0.6397 (m-80) REVERT: D 119 GLU cc_start: 0.8776 (tp30) cc_final: 0.8513 (tp30) REVERT: D 139 LEU cc_start: 0.7857 (mt) cc_final: 0.7639 (mp) REVERT: E 1 MET cc_start: 0.6206 (mmt) cc_final: 0.5258 (ptm) REVERT: E 17 MET cc_start: 0.8262 (mmm) cc_final: 0.8014 (mmt) REVERT: E 51 ILE cc_start: 0.8478 (mm) cc_final: 0.8155 (tp) REVERT: F 123 LEU cc_start: 0.4200 (OUTLIER) cc_final: 0.3969 (tp) REVERT: F 285 MET cc_start: 0.6109 (tmm) cc_final: 0.5868 (tmm) REVERT: F 293 PHE cc_start: 0.7816 (OUTLIER) cc_final: 0.7406 (m-80) REVERT: F 319 TYR cc_start: 0.7184 (m-10) cc_final: 0.6900 (m-80) REVERT: F 336 HIS cc_start: 0.7983 (m90) cc_final: 0.7100 (m90) outliers start: 33 outliers final: 24 residues processed: 194 average time/residue: 0.1138 time to fit residues: 33.8077 Evaluate side-chains 189 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 181 ASP Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 293 PHE Chi-restraints excluded: chain F residue 356 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 243 GLN D 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.161996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.109168 restraints weight = 18746.228| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.87 r_work: 0.3104 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15038 Z= 0.183 Angle : 0.571 11.897 20422 Z= 0.291 Chirality : 0.043 0.148 2306 Planarity : 0.005 0.059 2567 Dihedral : 7.299 69.108 2151 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.94 % Allowed : 16.07 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.35 (0.19), residues: 1880 helix: 1.31 (0.18), residues: 846 sheet: -2.11 (0.38), residues: 163 loop : -1.43 (0.20), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 118 TYR 0.018 0.001 TYR B 360 PHE 0.023 0.002 PHE D 50 TRP 0.032 0.002 TRP F 308 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.18 (15035) covalent geometry : angle 0.56867 / 0.29 (20418) hydrogen bonds : bond 0.04601 / 3.00 ( 671) hydrogen bonds : angle 4.34267 / 2.94 ( 1938) metal coordination : bond 0.01455 / 0.74 ( 3) metal coordination : angle 3.77152 / 2.04 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8864 (mttp) cc_final: 0.8199 (mttm) REVERT: B 151 ARG cc_start: 0.5745 (mmm160) cc_final: 0.4588 (ptp-110) REVERT: B 152 LYS cc_start: 0.8910 (ttmt) cc_final: 0.8128 (tppt) REVERT: C 51 GLN cc_start: 0.8399 (tm-30) cc_final: 0.8131 (tm-30) REVERT: C 74 ARG cc_start: 0.7292 (mmt180) cc_final: 0.6950 (mtt-85) REVERT: D 18 ASN cc_start: 0.8438 (t0) cc_final: 0.7952 (t0) REVERT: D 50 PHE cc_start: 0.7650 (t80) cc_final: 0.6283 (m-80) REVERT: D 119 GLU cc_start: 0.8783 (tp30) cc_final: 0.8487 (tp30) REVERT: D 139 LEU cc_start: 0.7879 (mt) cc_final: 0.7643 (mp) REVERT: D 146 MET cc_start: 0.7590 (mmt) cc_final: 0.7095 (mmt) REVERT: E 1 MET cc_start: 0.6137 (mmt) cc_final: 0.5223 (ptm) REVERT: E 17 MET cc_start: 0.8299 (mmm) cc_final: 0.8036 (mmt) REVERT: E 51 ILE cc_start: 0.8503 (mm) cc_final: 0.8069 (tp) REVERT: F 123 LEU cc_start: 0.4178 (OUTLIER) cc_final: 0.3965 (tp) REVERT: F 285 MET cc_start: 0.6270 (tmm) cc_final: 0.6009 (tmm) REVERT: F 293 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.7456 (m-80) REVERT: F 319 TYR cc_start: 0.7165 (m-10) cc_final: 0.6905 (m-80) outliers start: 30 outliers final: 22 residues processed: 188 average time/residue: 0.1050 time to fit residues: 30.6393 Evaluate side-chains 187 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 293 PHE Chi-restraints excluded: chain F residue 356 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 21 optimal weight: 0.9990 chunk 88 optimal weight: 0.3980 chunk 115 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 152 optimal weight: 50.0000 chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 151 optimal weight: 8.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 243 GLN C 68 ASN D 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.166437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.113864 restraints weight = 18721.494| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.83 r_work: 0.3168 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15038 Z= 0.109 Angle : 0.519 12.180 20422 Z= 0.265 Chirality : 0.041 0.213 2306 Planarity : 0.004 0.059 2567 Dihedral : 7.110 70.282 2151 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.88 % Allowed : 16.33 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.07 (0.20), residues: 1880 helix: 1.64 (0.19), residues: 841 sheet: -2.01 (0.39), residues: 156 loop : -1.38 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 408 TYR 0.013 0.001 TYR D 141 PHE 0.021 0.001 PHE D 50 TRP 0.035 0.002 TRP F 308 HIS 0.002 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (15035) covalent geometry : angle 0.51718 / 0.26 (20418) hydrogen bonds : bond 0.03811 / 2.47 ( 671) hydrogen bonds : angle 4.18958 / 2.84 ( 1938) metal coordination : bond 0.00656 / 0.33 ( 3) metal coordination : angle 2.79396 / 1.60 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8924 (mttp) cc_final: 0.8317 (mttm) REVERT: B 151 ARG cc_start: 0.5643 (mmm160) cc_final: 0.4764 (ptp-110) REVERT: B 152 LYS cc_start: 0.9019 (ttmt) cc_final: 0.8302 (tppt) REVERT: C 51 GLN cc_start: 0.8491 (tm-30) cc_final: 0.8220 (tm-30) REVERT: C 74 ARG cc_start: 0.7378 (mmt180) cc_final: 0.7030 (mtt-85) REVERT: D 18 ASN cc_start: 0.8495 (t0) cc_final: 0.8028 (t0) REVERT: D 50 PHE cc_start: 0.7787 (t80) cc_final: 0.6593 (m-80) REVERT: D 119 GLU cc_start: 0.8779 (tp30) cc_final: 0.8552 (tp30) REVERT: D 139 LEU cc_start: 0.8029 (mt) cc_final: 0.7819 (mp) REVERT: D 146 MET cc_start: 0.7538 (mmt) cc_final: 0.7156 (mmt) REVERT: E 1 MET cc_start: 0.6290 (mmt) cc_final: 0.5399 (ptm) REVERT: E 51 ILE cc_start: 0.8632 (mm) cc_final: 0.8308 (tp) REVERT: F 123 LEU cc_start: 0.4245 (OUTLIER) cc_final: 0.4032 (tp) REVERT: F 293 PHE cc_start: 0.7845 (OUTLIER) cc_final: 0.7440 (m-80) REVERT: F 319 TYR cc_start: 0.7215 (m-10) cc_final: 0.6964 (m-80) outliers start: 29 outliers final: 21 residues processed: 192 average time/residue: 0.0959 time to fit residues: 28.3837 Evaluate side-chains 187 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 293 PHE Chi-restraints excluded: chain F residue 356 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 50 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 243 GLN C 141 HIS D 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.165107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.112461 restraints weight = 18685.868| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.83 r_work: 0.3152 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15038 Z= 0.139 Angle : 0.549 12.109 20422 Z= 0.277 Chirality : 0.042 0.159 2306 Planarity : 0.004 0.060 2567 Dihedral : 7.086 69.300 2151 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.62 % Allowed : 16.59 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.20), residues: 1880 helix: 1.53 (0.18), residues: 846 sheet: -1.99 (0.39), residues: 156 loop : -1.35 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 408 TYR 0.015 0.001 TYR B 360 PHE 0.022 0.001 PHE D 50 TRP 0.030 0.002 TRP F 308 HIS 0.006 0.001 HIS C 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (15035) covalent geometry : angle 0.54690 / 0.28 (20418) hydrogen bonds : bond 0.04124 / 2.69 ( 671) hydrogen bonds : angle 4.22844 / 2.87 ( 1938) metal coordination : bond 0.00934 / 0.48 ( 3) metal coordination : angle 3.10174 / 1.68 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8880 (mttp) cc_final: 0.8231 (mttm) REVERT: B 151 ARG cc_start: 0.5664 (mmm160) cc_final: 0.4574 (ptp-110) REVERT: B 152 LYS cc_start: 0.8962 (ttmt) cc_final: 0.8203 (tppt) REVERT: C 51 GLN cc_start: 0.8443 (tm-30) cc_final: 0.8169 (tm-30) REVERT: C 74 ARG cc_start: 0.7260 (mmt180) cc_final: 0.6909 (mtt-85) REVERT: D 18 ASN cc_start: 0.8428 (t0) cc_final: 0.7931 (t0) REVERT: D 50 PHE cc_start: 0.7659 (t80) cc_final: 0.6368 (m-80) REVERT: D 119 GLU cc_start: 0.8784 (tp30) cc_final: 0.8510 (tp30) REVERT: D 139 LEU cc_start: 0.7900 (mt) cc_final: 0.7671 (mp) REVERT: D 146 MET cc_start: 0.7553 (mmt) cc_final: 0.7163 (mmt) REVERT: E 1 MET cc_start: 0.6183 (mmt) cc_final: 0.5237 (ptm) REVERT: E 51 ILE cc_start: 0.8533 (mm) cc_final: 0.8140 (tp) REVERT: F 123 LEU cc_start: 0.4014 (OUTLIER) cc_final: 0.3810 (tp) REVERT: F 214 MET cc_start: 0.5129 (mpp) cc_final: 0.4832 (mpp) REVERT: F 293 PHE cc_start: 0.7782 (OUTLIER) cc_final: 0.7393 (m-80) outliers start: 25 outliers final: 21 residues processed: 183 average time/residue: 0.1083 time to fit residues: 30.7945 Evaluate side-chains 186 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 293 PHE Chi-restraints excluded: chain F residue 356 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 63 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 158 optimal weight: 20.0000 chunk 89 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 243 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.163764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.111183 restraints weight = 18671.833| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.83 r_work: 0.3134 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15038 Z= 0.169 Angle : 0.567 12.049 20422 Z= 0.287 Chirality : 0.043 0.160 2306 Planarity : 0.004 0.062 2567 Dihedral : 7.151 68.672 2151 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.62 % Allowed : 16.66 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.17 (0.19), residues: 1880 helix: 1.41 (0.18), residues: 851 sheet: -1.99 (0.38), residues: 165 loop : -1.30 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 118 TYR 0.016 0.001 TYR B 360 PHE 0.022 0.001 PHE D 50 TRP 0.029 0.002 TRP F 308 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 (15035) covalent geometry : angle 0.56460 / 0.29 (20418) hydrogen bonds : bond 0.04415 / 2.87 ( 671) hydrogen bonds : angle 4.28145 / 2.90 ( 1938) metal coordination : bond 0.01473 / 0.75 ( 3) metal coordination : angle 3.95278 / 2.18 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3879.85 seconds wall clock time: 67 minutes 12.07 seconds (4032.07 seconds total)