Starting phenix.real_space_refine on Thu Mar 5 17:49:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jzz_22585/03_2026/7jzz_22585.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jzz_22585/03_2026/7jzz_22585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jzz_22585/03_2026/7jzz_22585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jzz_22585/03_2026/7jzz_22585.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jzz_22585/03_2026/7jzz_22585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jzz_22585/03_2026/7jzz_22585.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 60 5.49 5 S 31 5.16 5 C 15000 2.51 5 N 4405 2.21 5 O 4701 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 138 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24197 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3088 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 24, 'TRANS': 402} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 356 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 297 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ASP:plan': 11, 'GLN:plan1': 9, 'GLU:plan': 9, 'ARG:plan': 11, 'HIS:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 234 Chain: "B" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2411 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 24, 'TRANS': 281} Chain breaks: 1 Chain: "C" Number of atoms: 1448 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 1480 Chain: "D" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2307 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 10, 'TRANS': 287} Chain breaks: 2 Chain: "E" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "F" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "G" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "H" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2554 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain breaks: 1 Chain: "I" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "J" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 374 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "K" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 374 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "M" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1273 Classifications: {'DNA': 1, 'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 28, 'rna3p': 32} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 5.86, per 1000 atoms: 0.24 Number of scatterers: 24197 At special positions: 0 Unit cell: (131.25, 156.45, 148.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 P 60 15.00 O 4701 8.00 N 4405 7.00 C 15000 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 1.1 seconds 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5534 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 54 sheets defined 33.3% alpha, 20.6% beta 6 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 2.89 Creating SS restraints... Processing helix chain 'A' and resid 9 through 31 Processing helix chain 'A' and resid 38 through 47 removed outlier: 4.072A pdb=" N THR A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 60 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 114 through 122 removed outlier: 4.312A pdb=" N PHE A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 removed outlier: 3.766A pdb=" N GLU A 136 " --> pdb=" O ASN A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 161 removed outlier: 3.756A pdb=" N ALA A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY A 161 " --> pdb=" O GLN A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 196 through 211 Processing helix chain 'A' and resid 212 through 225 removed outlier: 3.668A pdb=" N ALA A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.521A pdb=" N ILE A 251 " --> pdb=" O PRO A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 258 removed outlier: 4.070A pdb=" N GLU A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 removed outlier: 4.497A pdb=" N GLN A 273 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 294 through 306 removed outlier: 3.553A pdb=" N SER A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 344 removed outlier: 4.506A pdb=" N ALA A 317 " --> pdb=" O HIS A 313 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 Processing helix chain 'A' and resid 363 through 369 removed outlier: 3.748A pdb=" N ALA A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.821A pdb=" N GLY A 381 " --> pdb=" O ARG A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 removed outlier: 4.080A pdb=" N ARG A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 409 through 430 Processing helix chain 'B' and resid 33 through 49 removed outlier: 3.955A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 removed outlier: 3.903A pdb=" N ASP B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 165 through 180 Processing helix chain 'B' and resid 189 through 204 removed outlier: 3.901A pdb=" N LEU B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 218 Processing helix chain 'C' and resid 16 through 36 removed outlier: 3.503A pdb=" N LEU C 20 " --> pdb=" O PRO C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 72 removed outlier: 3.917A pdb=" N ALA C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.506A pdb=" N LEU C 76 " --> pdb=" O ARG C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 121 Processing helix chain 'C' and resid 123 through 131 Processing helix chain 'C' and resid 132 through 136 removed outlier: 4.012A pdb=" N VAL C 135 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA C 136 " --> pdb=" O ASP C 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 132 through 136' Processing helix chain 'D' and resid 51 through 55 Processing helix chain 'D' and resid 130 through 148 Processing helix chain 'D' and resid 151 through 163 Processing helix chain 'D' and resid 208 through 223 removed outlier: 3.788A pdb=" N ALA D 213 " --> pdb=" O ALA D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 322 through 332 removed outlier: 3.542A pdb=" N LEU D 326 " --> pdb=" O ASP D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 82 through 92 removed outlier: 3.732A pdb=" N SER E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 148 Processing helix chain 'E' and resid 151 through 163 Processing helix chain 'E' and resid 209 through 223 removed outlier: 3.506A pdb=" N ALA E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 284 Processing helix chain 'E' and resid 293 through 297 removed outlier: 3.627A pdb=" N LEU E 296 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY E 297 " --> pdb=" O ASP E 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 293 through 297' Processing helix chain 'E' and resid 322 through 332 Processing helix chain 'E' and resid 338 through 352 Processing helix chain 'F' and resid 51 through 55 Processing helix chain 'F' and resid 82 through 91 Processing helix chain 'F' and resid 130 through 148 Processing helix chain 'F' and resid 151 through 163 removed outlier: 3.506A pdb=" N ARG F 155 " --> pdb=" O ALA F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 223 Processing helix chain 'F' and resid 275 through 284 Processing helix chain 'F' and resid 293 through 297 removed outlier: 3.728A pdb=" N LEU F 296 " --> pdb=" O GLU F 293 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY F 297 " --> pdb=" O ASP F 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 293 through 297' Processing helix chain 'F' and resid 322 through 332 Processing helix chain 'F' and resid 338 through 352 Processing helix chain 'G' and resid 82 through 91 Processing helix chain 'G' and resid 130 through 148 Processing helix chain 'G' and resid 151 through 163 Processing helix chain 'G' and resid 209 through 223 removed outlier: 3.556A pdb=" N ALA G 213 " --> pdb=" O ALA G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 275 through 284 Processing helix chain 'G' and resid 322 through 332 Processing helix chain 'G' and resid 338 through 352 Processing helix chain 'H' and resid 51 through 55 Processing helix chain 'H' and resid 82 through 92 removed outlier: 3.606A pdb=" N SER H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 148 Processing helix chain 'H' and resid 150 through 163 removed outlier: 3.526A pdb=" N ALA H 154 " --> pdb=" O PHE H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 223 Processing helix chain 'H' and resid 275 through 284 Processing helix chain 'H' and resid 322 through 331 removed outlier: 3.566A pdb=" N LEU H 326 " --> pdb=" O ASP H 322 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 352 Processing helix chain 'I' and resid 51 through 55 Processing helix chain 'I' and resid 82 through 90 Processing helix chain 'I' and resid 130 through 148 Processing helix chain 'I' and resid 152 through 163 Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 275 through 284 Processing helix chain 'I' and resid 322 through 332 removed outlier: 3.638A pdb=" N LEU I 326 " --> pdb=" O ASP I 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 352 Processing helix chain 'J' and resid 109 through 121 Processing helix chain 'K' and resid 109 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 69 Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 192 removed outlier: 6.251A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 192 removed outlier: 6.251A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY B 254 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N GLY B 285 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLY B 287 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N TRP B 289 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LEU B 248 " --> pdb=" O TRP B 289 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 267 removed outlier: 5.861A pdb=" N LEU A 265 " --> pdb=" O TRP B 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 54 through 61 removed outlier: 4.012A pdb=" N VAL B 59 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU B 110 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 65 through 68 removed outlier: 5.093A pdb=" N ALA B 103 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN B 19 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER B 16 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA9, first strand: chain 'B' and resid 221 through 222 Processing sheet with id=AB1, first strand: chain 'B' and resid 304 through 306 removed outlier: 3.617A pdb=" N SER B 317 " --> pdb=" O TYR B 304 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 41 through 43 removed outlier: 3.501A pdb=" N HIS C 3 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 41 through 43 removed outlier: 3.501A pdb=" N HIS C 3 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AB5, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB6, first strand: chain 'C' and resid 172 through 173 removed outlier: 3.876A pdb=" N GLY C 172 " --> pdb=" O LYS C 180 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 127 through 128 Processing sheet with id=AB8, first strand: chain 'D' and resid 38 through 39 removed outlier: 4.058A pdb=" N VAL D 228 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG D 191 " --> pdb=" O HIS D 183 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 38 through 39 Processing sheet with id=AC1, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AC2, first strand: chain 'D' and resid 248 through 249 removed outlier: 4.300A pdb=" N THR D 264 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 285 through 287 Processing sheet with id=AC4, first strand: chain 'D' and resid 306 through 307 Processing sheet with id=AC5, first strand: chain 'E' and resid 127 through 128 Processing sheet with id=AC6, first strand: chain 'E' and resid 38 through 39 removed outlier: 4.103A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU E 229 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL E 177 " --> pdb=" O ASP E 196 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASP E 196 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL E 179 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARG E 194 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE E 181 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA E 192 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N HIS E 183 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 38 through 39 Processing sheet with id=AC8, first strand: chain 'E' and resid 63 through 70 Processing sheet with id=AC9, first strand: chain 'E' and resid 248 through 249 removed outlier: 4.417A pdb=" N THR E 264 " --> pdb=" O GLU E 249 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 285 through 287 Processing sheet with id=AD2, first strand: chain 'E' and resid 306 through 307 removed outlier: 3.741A pdb=" N LYS E 312 " --> pdb=" O VAL E 307 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 127 through 128 Processing sheet with id=AD4, first strand: chain 'F' and resid 38 through 39 removed outlier: 4.095A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU F 229 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL F 177 " --> pdb=" O ASP F 196 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ASP F 196 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL F 179 " --> pdb=" O ARG F 194 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG F 194 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE F 181 " --> pdb=" O ALA F 192 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ALA F 192 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N HIS F 183 " --> pdb=" O ALA F 190 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 38 through 39 Processing sheet with id=AD6, first strand: chain 'F' and resid 63 through 70 Processing sheet with id=AD7, first strand: chain 'F' and resid 285 through 287 Processing sheet with id=AD8, first strand: chain 'F' and resid 306 through 307 removed outlier: 3.658A pdb=" N LYS F 312 " --> pdb=" O VAL F 307 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 127 through 128 Processing sheet with id=AE1, first strand: chain 'G' and resid 38 through 39 removed outlier: 4.209A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL G 177 " --> pdb=" O ASP G 196 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ASP G 196 " --> pdb=" O VAL G 177 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL G 179 " --> pdb=" O ARG G 194 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG G 194 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE G 181 " --> pdb=" O ALA G 192 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA G 192 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N HIS G 183 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 38 through 39 Processing sheet with id=AE3, first strand: chain 'G' and resid 64 through 70 removed outlier: 4.284A pdb=" N PHE J 104 " --> pdb=" O LEU G 95 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N THR G 97 " --> pdb=" O PHE J 104 " (cutoff:3.500A) removed outlier: 11.660A pdb=" N CYS J 106 " --> pdb=" O THR G 97 " (cutoff:3.500A) removed outlier: 14.496A pdb=" N ASP G 99 " --> pdb=" O CYS J 106 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N PHE J 104 " --> pdb=" O LYS J 94 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LYS J 94 " --> pdb=" O PHE J 104 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 248 through 249 removed outlier: 4.600A pdb=" N THR G 264 " --> pdb=" O GLU G 249 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 285 through 287 Processing sheet with id=AE6, first strand: chain 'G' and resid 306 through 307 Processing sheet with id=AE7, first strand: chain 'H' and resid 127 through 128 Processing sheet with id=AE8, first strand: chain 'H' and resid 38 through 39 removed outlier: 4.055A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG H 191 " --> pdb=" O HIS H 183 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 38 through 39 Processing sheet with id=AF1, first strand: chain 'H' and resid 63 through 70 removed outlier: 3.579A pdb=" N ASN H 94 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA H 101 " --> pdb=" O VAL H 244 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 285 through 287 Processing sheet with id=AF3, first strand: chain 'H' and resid 306 through 307 removed outlier: 3.535A pdb=" N LYS H 312 " --> pdb=" O VAL H 307 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 127 through 128 Processing sheet with id=AF5, first strand: chain 'I' and resid 38 through 39 removed outlier: 4.697A pdb=" N LEU I 229 " --> pdb=" O ILE I 184 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 189 through 192 removed outlier: 6.666A pdb=" N HIS I 183 " --> pdb=" O ALA I 190 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA I 192 " --> pdb=" O ILE I 181 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE I 181 " --> pdb=" O ALA I 192 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU I 229 " --> pdb=" O ILE I 184 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 63 through 70 removed outlier: 3.583A pdb=" N VAL I 68 " --> pdb=" O GLN I 96 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA I 101 " --> pdb=" O VAL I 244 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 63 through 70 removed outlier: 3.583A pdb=" N VAL I 68 " --> pdb=" O GLN I 96 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N THR I 97 " --> pdb=" O PHE K 104 " (cutoff:3.500A) removed outlier: 11.844A pdb=" N CYS K 106 " --> pdb=" O THR I 97 " (cutoff:3.500A) removed outlier: 14.427A pdb=" N ASP I 99 " --> pdb=" O CYS K 106 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N PHE K 104 " --> pdb=" O LYS K 94 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LYS K 94 " --> pdb=" O PHE K 104 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 285 through 287 1022 hydrogen bonds defined for protein. 2802 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 4.47 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5057 1.32 - 1.45: 6221 1.45 - 1.57: 13363 1.57 - 1.70: 120 1.70 - 1.82: 46 Bond restraints: 24807 Sorted by residual: bond pdb=" O3' A M 36 " pdb=" P C M 37 " ideal model delta sigma weight residual 1.607 1.675 -0.068 1.50e-02 4.44e+03 2.05e+01 bond pdb=" C LEU B 181 " pdb=" N PRO B 182 " ideal model delta sigma weight residual 1.337 1.378 -0.041 9.80e-03 1.04e+04 1.77e+01 bond pdb=" CB ARG G 237 " pdb=" CG ARG G 237 " ideal model delta sigma weight residual 1.520 1.432 0.088 3.00e-02 1.11e+03 8.56e+00 bond pdb=" N LEU H 250 " pdb=" CA LEU H 250 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.22e-02 6.72e+03 7.35e+00 bond pdb=" CB ILE H 238 " pdb=" CG2 ILE H 238 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.47e+00 ... (remaining 24802 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 32393 2.08 - 4.16: 1337 4.16 - 6.23: 178 6.23 - 8.31: 42 8.31 - 10.39: 9 Bond angle restraints: 33959 Sorted by residual: angle pdb=" C ILE F 251 " pdb=" N LEU F 252 " pdb=" CA LEU F 252 " ideal model delta sigma weight residual 120.44 128.28 -7.84 1.30e+00 5.92e-01 3.63e+01 angle pdb=" C GLU D 188 " pdb=" N VAL D 189 " pdb=" CA VAL D 189 " ideal model delta sigma weight residual 121.97 126.85 -4.88 1.00e+00 1.00e+00 2.38e+01 angle pdb=" C LYS H 77 " pdb=" N THR H 78 " pdb=" CA THR H 78 " ideal model delta sigma weight residual 121.54 130.83 -9.29 1.91e+00 2.74e-01 2.36e+01 angle pdb=" C GLN A 124 " pdb=" N TYR A 125 " pdb=" CA TYR A 125 " ideal model delta sigma weight residual 120.79 127.48 -6.69 1.39e+00 5.18e-01 2.32e+01 angle pdb=" N GLY H 356 " pdb=" CA GLY H 356 " pdb=" C GLY H 356 " ideal model delta sigma weight residual 111.95 107.48 4.47 9.50e-01 1.11e+00 2.22e+01 ... (remaining 33954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 14475 35.93 - 71.86: 461 71.86 - 107.79: 32 107.79 - 143.72: 3 143.72 - 179.65: 4 Dihedral angle restraints: 14975 sinusoidal: 6401 harmonic: 8574 Sorted by residual: dihedral pdb=" O4' U M 21 " pdb=" C1' U M 21 " pdb=" N1 U M 21 " pdb=" C2 U M 21 " ideal model delta sinusoidal sigma weight residual 200.00 60.96 139.04 1 1.50e+01 4.44e-03 7.49e+01 dihedral pdb=" O4' U M 33 " pdb=" C1' U M 33 " pdb=" N1 U M 33 " pdb=" C2 U M 33 " ideal model delta sinusoidal sigma weight residual 200.00 72.55 127.45 1 1.50e+01 4.44e-03 6.86e+01 dihedral pdb=" O4' C M 37 " pdb=" C1' C M 37 " pdb=" N1 C M 37 " pdb=" C2 C M 37 " ideal model delta sinusoidal sigma weight residual -128.00 51.65 -179.65 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 14972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2710 0.053 - 0.106: 882 0.106 - 0.158: 194 0.158 - 0.211: 22 0.211 - 0.264: 7 Chirality restraints: 3815 Sorted by residual: chirality pdb=" C3' U M 33 " pdb=" C4' U M 33 " pdb=" O3' U M 33 " pdb=" C2' U M 33 " both_signs ideal model delta sigma weight residual False -2.48 -2.74 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CG LEU B 197 " pdb=" CB LEU B 197 " pdb=" CD1 LEU B 197 " pdb=" CD2 LEU B 197 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CB ILE C 60 " pdb=" CA ILE C 60 " pdb=" CG1 ILE C 60 " pdb=" CG2 ILE C 60 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 3812 not shown) Planarity restraints: 4261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER K 96 " 0.052 5.00e-02 4.00e+02 7.96e-02 1.01e+01 pdb=" N PRO K 97 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO K 97 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO K 97 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER J 96 " -0.052 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO J 97 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO J 97 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO J 97 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 294 " 0.049 5.00e-02 4.00e+02 7.35e-02 8.63e+00 pdb=" N PRO A 295 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.041 5.00e-02 4.00e+02 ... (remaining 4258 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3690 2.75 - 3.29: 21875 3.29 - 3.82: 42249 3.82 - 4.36: 51039 4.36 - 4.90: 86828 Nonbonded interactions: 205681 Sorted by model distance: nonbonded pdb=" OH TYR G 324 " pdb=" O SER H 73 " model vdw 2.209 3.040 nonbonded pdb=" OH TYR E 324 " pdb=" O SER F 73 " model vdw 2.227 3.040 nonbonded pdb=" OH TYR D 324 " pdb=" O SER E 73 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR H 324 " pdb=" O SER I 73 " model vdw 2.260 3.040 nonbonded pdb=" OH TYR F 324 " pdb=" O SER G 73 " model vdw 2.266 3.040 ... (remaining 205676 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = (chain 'E' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'F' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'G' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'H' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'I' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) } ncs_group { reference = chain 'J' selection = chain 'K' } 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=0.37 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 24.560 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.088 24807 Z= 0.465 Angle : 0.977 10.390 33959 Z= 0.551 Chirality : 0.054 0.264 3815 Planarity : 0.007 0.080 4261 Dihedral : 17.227 179.653 9441 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.61 % Allowed : 9.21 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.65 (0.12), residues: 2949 helix: -2.63 (0.11), residues: 917 sheet: -1.09 (0.22), residues: 490 loop : -2.79 (0.12), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG G 117 TYR 0.039 0.003 TYR H 304 PHE 0.020 0.002 PHE C 155 TRP 0.034 0.002 TRP F 49 HIS 0.007 0.002 HIS D 343 Details of bonding type rmsd covalent geometry : bond 0.01049 (24807) covalent geometry : angle 0.97716 (33959) hydrogen bonds : bond 0.16789 ( 995) hydrogen bonds : angle 7.39777 ( 2830) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 332 time to evaluate : 0.965 Fit side-chains REVERT: A 200 HIS cc_start: 0.8299 (t-90) cc_final: 0.7685 (t-90) REVERT: A 235 TYR cc_start: 0.8279 (m-80) cc_final: 0.7967 (m-80) REVERT: A 331 ASP cc_start: 0.7145 (m-30) cc_final: 0.6455 (m-30) REVERT: A 424 MET cc_start: 0.8076 (mmm) cc_final: 0.7747 (mtt) REVERT: B 170 ARG cc_start: 0.7660 (ttp80) cc_final: 0.6709 (mtm110) REVERT: B 189 ARG cc_start: 0.8101 (mtp85) cc_final: 0.7881 (mtp85) REVERT: B 218 ARG cc_start: 0.7608 (ptt180) cc_final: 0.7208 (ptt-90) REVERT: B 268 ARG cc_start: 0.7511 (tpt170) cc_final: 0.7145 (ttt90) REVERT: C 84 GLN cc_start: 0.7923 (pt0) cc_final: 0.7680 (pt0) REVERT: C 110 GLU cc_start: 0.8138 (mp0) cc_final: 0.7929 (mp0) REVERT: C 143 PHE cc_start: 0.7368 (p90) cc_final: 0.6610 (p90) REVERT: D 294 ASP cc_start: 0.7660 (t0) cc_final: 0.7455 (t0) REVERT: F 77 LYS cc_start: 0.8285 (mtpt) cc_final: 0.8066 (mtmt) REVERT: F 258 LYS cc_start: 0.7346 (mmpt) cc_final: 0.6880 (mmpt) REVERT: F 269 ARG cc_start: 0.7609 (ptp-170) cc_final: 0.7403 (ptp-170) REVERT: H 72 ILE cc_start: 0.8914 (tp) cc_final: 0.8641 (tp) REVERT: H 94 ASN cc_start: 0.8251 (p0) cc_final: 0.7287 (t0) REVERT: I 99 ASP cc_start: 0.8349 (m-30) cc_final: 0.7877 (m-30) REVERT: I 185 ARG cc_start: 0.7770 (tpp80) cc_final: 0.7386 (mmt90) REVERT: I 249 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7871 (mt-10) REVERT: I 261 LYS cc_start: 0.7860 (mttt) cc_final: 0.7537 (mttt) REVERT: I 329 ASN cc_start: 0.7849 (m-40) cc_final: 0.7626 (m-40) REVERT: J 114 ASN cc_start: 0.8355 (m-40) cc_final: 0.8053 (m-40) REVERT: K 82 LYS cc_start: 0.8737 (ttmt) cc_final: 0.8233 (ttmt) REVERT: K 90 ASN cc_start: 0.8197 (t0) cc_final: 0.7680 (t0) outliers start: 14 outliers final: 4 residues processed: 341 average time/residue: 0.2260 time to fit residues: 110.0180 Evaluate side-chains 229 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 225 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 300 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.0980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS B 19 ASN ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN C 108 ASN C 120 HIS ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN F 348 ASN G 51 GLN ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 159 HIS H 348 ASN I 102 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.138443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.095273 restraints weight = 33741.488| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.15 r_work: 0.2796 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2584 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2584 r_free = 0.2584 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2584 r_free = 0.2584 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2584 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24807 Z= 0.132 Angle : 0.582 9.555 33959 Z= 0.306 Chirality : 0.040 0.193 3815 Planarity : 0.005 0.058 4261 Dihedral : 15.407 179.381 4201 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.56 % Allowed : 12.13 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.14), residues: 2949 helix: -0.53 (0.15), residues: 927 sheet: -0.68 (0.22), residues: 492 loop : -2.42 (0.13), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 69 TYR 0.018 0.001 TYR C 97 PHE 0.022 0.001 PHE A 391 TRP 0.013 0.001 TRP G 49 HIS 0.006 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00281 (24807) covalent geometry : angle 0.58208 (33959) hydrogen bonds : bond 0.03734 ( 995) hydrogen bonds : angle 5.17947 ( 2830) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 280 time to evaluate : 0.898 Fit side-chains REVERT: A 62 GLN cc_start: 0.7802 (mp10) cc_final: 0.7508 (mp10) REVERT: A 200 HIS cc_start: 0.8419 (t-90) cc_final: 0.7772 (t-170) REVERT: A 235 TYR cc_start: 0.8223 (m-80) cc_final: 0.7763 (m-80) REVERT: B 189 ARG cc_start: 0.8263 (mtp85) cc_final: 0.7959 (mtp85) REVERT: B 218 ARG cc_start: 0.7475 (ptt180) cc_final: 0.6981 (ptt-90) REVERT: B 268 ARG cc_start: 0.7621 (tpt170) cc_final: 0.7227 (ttt90) REVERT: C 44 PHE cc_start: 0.8567 (m-80) cc_final: 0.8307 (m-10) REVERT: C 84 GLN cc_start: 0.7807 (pt0) cc_final: 0.7539 (pt0) REVERT: C 143 PHE cc_start: 0.7127 (p90) cc_final: 0.6220 (p90) REVERT: D 294 ASP cc_start: 0.7955 (t0) cc_final: 0.7639 (t0) REVERT: F 51 GLN cc_start: 0.8210 (pt0) cc_final: 0.7993 (pt0) REVERT: F 77 LYS cc_start: 0.8251 (mtpt) cc_final: 0.8050 (mtmt) REVERT: F 188 GLU cc_start: 0.8486 (pm20) cc_final: 0.8215 (pm20) REVERT: G 188 GLU cc_start: 0.8098 (mp0) cc_final: 0.7863 (mm-30) REVERT: G 206 LYS cc_start: 0.8392 (mmmt) cc_final: 0.7854 (mtmt) REVERT: H 72 ILE cc_start: 0.9027 (tp) cc_final: 0.8771 (tp) REVERT: H 94 ASN cc_start: 0.8466 (p0) cc_final: 0.7631 (t0) REVERT: I 34 GLU cc_start: 0.8884 (tt0) cc_final: 0.8679 (tt0) REVERT: I 73 SER cc_start: 0.9129 (m) cc_final: 0.8496 (p) REVERT: I 185 ARG cc_start: 0.7823 (tpp80) cc_final: 0.7433 (tpp-160) REVERT: I 254 LYS cc_start: 0.7907 (mmtt) cc_final: 0.7421 (mppt) REVERT: J 90 ASN cc_start: 0.8426 (t0) cc_final: 0.7992 (t0) REVERT: J 99 HIS cc_start: 0.8242 (OUTLIER) cc_final: 0.7624 (p-80) REVERT: J 114 ASN cc_start: 0.8250 (m-40) cc_final: 0.8024 (m-40) REVERT: K 82 LYS cc_start: 0.8785 (ttmt) cc_final: 0.8516 (tttm) REVERT: K 90 ASN cc_start: 0.8627 (t0) cc_final: 0.8193 (t0) REVERT: K 99 HIS cc_start: 0.8139 (OUTLIER) cc_final: 0.5840 (p-80) outliers start: 36 outliers final: 19 residues processed: 306 average time/residue: 0.1979 time to fit residues: 89.9801 Evaluate side-chains 263 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 242 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 348 ASN Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain J residue 99 HIS Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain K residue 99 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 162 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 56 optimal weight: 0.0060 chunk 138 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 252 optimal weight: 6.9990 chunk 256 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 159 optimal weight: 0.8980 chunk 58 optimal weight: 20.0000 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 ASN ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 ASN ** I 159 HIS ** 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 = 0.3655 r_free = 0.3655 target = 0.138643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.095435 restraints weight = 36349.680| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.27 r_work: 0.2787 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24807 Z= 0.129 Angle : 0.541 8.037 33959 Z= 0.283 Chirality : 0.040 0.182 3815 Planarity : 0.004 0.050 4261 Dihedral : 15.190 179.768 4199 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.26 % Allowed : 12.91 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.14), residues: 2949 helix: 0.48 (0.16), residues: 925 sheet: -0.37 (0.23), residues: 491 loop : -2.23 (0.14), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 237 TYR 0.012 0.001 TYR F 290 PHE 0.015 0.001 PHE B 184 TRP 0.015 0.001 TRP A 394 HIS 0.009 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00284 (24807) covalent geometry : angle 0.54147 (33959) hydrogen bonds : bond 0.03271 ( 995) hydrogen bonds : angle 4.77052 ( 2830) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 256 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 62 GLN cc_start: 0.7790 (mp10) cc_final: 0.7443 (mp10) REVERT: A 200 HIS cc_start: 0.8423 (t-90) cc_final: 0.7903 (t-90) REVERT: A 228 TRP cc_start: 0.7732 (t-100) cc_final: 0.7302 (t-100) REVERT: A 235 TYR cc_start: 0.8130 (m-80) cc_final: 0.7668 (m-80) REVERT: A 257 GLU cc_start: 0.7988 (mp0) cc_final: 0.7360 (mp0) REVERT: B 184 PHE cc_start: 0.8646 (m-80) cc_final: 0.8383 (m-80) REVERT: B 189 ARG cc_start: 0.8246 (mtp85) cc_final: 0.7929 (mtp85) REVERT: B 268 ARG cc_start: 0.7553 (tpt170) cc_final: 0.7198 (ttt90) REVERT: B 306 HIS cc_start: 0.7893 (m-70) cc_final: 0.7686 (m-70) REVERT: C 143 PHE cc_start: 0.6997 (p90) cc_final: 0.6111 (p90) REVERT: D 212 ASP cc_start: 0.8060 (m-30) cc_final: 0.7813 (m-30) REVERT: D 294 ASP cc_start: 0.7844 (t0) cc_final: 0.7556 (t0) REVERT: F 188 GLU cc_start: 0.8378 (pm20) cc_final: 0.7908 (pm20) REVERT: F 258 LYS cc_start: 0.7133 (mmpt) cc_final: 0.6764 (mmpt) REVERT: F 269 ARG cc_start: 0.8217 (ptp-170) cc_final: 0.7941 (mtm180) REVERT: G 188 GLU cc_start: 0.8064 (mp0) cc_final: 0.7821 (mm-30) REVERT: G 206 LYS cc_start: 0.8342 (mmmt) cc_final: 0.7883 (mtmt) REVERT: H 72 ILE cc_start: 0.9051 (tp) cc_final: 0.8826 (tp) REVERT: H 94 ASN cc_start: 0.8433 (p0) cc_final: 0.7583 (t0) REVERT: I 34 GLU cc_start: 0.8850 (tt0) cc_final: 0.8475 (tt0) REVERT: I 147 ASP cc_start: 0.8353 (t70) cc_final: 0.8055 (m-30) REVERT: J 90 ASN cc_start: 0.8331 (t0) cc_final: 0.7917 (t0) REVERT: J 99 HIS cc_start: 0.8232 (OUTLIER) cc_final: 0.7455 (p-80) REVERT: K 82 LYS cc_start: 0.8799 (ttmt) cc_final: 0.8313 (tttm) REVERT: K 90 ASN cc_start: 0.8796 (t0) cc_final: 0.8314 (t0) REVERT: K 99 HIS cc_start: 0.8173 (OUTLIER) cc_final: 0.5697 (p-80) outliers start: 52 outliers final: 35 residues processed: 285 average time/residue: 0.1876 time to fit residues: 80.1618 Evaluate side-chains 264 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 227 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 414 TRP Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain F residue 146 ASN Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 237 ARG Chi-restraints excluded: chain G residue 304 TYR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 304 TYR Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 333 ARG Chi-restraints excluded: chain J residue 99 HIS Chi-restraints excluded: chain K residue 99 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 295 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 188 optimal weight: 0.3980 chunk 95 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 279 optimal weight: 4.9990 chunk 192 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 201 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS C 19 GLN ** C 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN C 108 ASN C 153 GLN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN E 148 GLN E 342 GLN G 148 GLN ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 348 ASN ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 ASN ** I 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 HIS I 348 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.139332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.096743 restraints weight = 35613.641| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.23 r_work: 0.2772 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24807 Z= 0.127 Angle : 0.529 8.029 33959 Z= 0.274 Chirality : 0.039 0.184 3815 Planarity : 0.004 0.049 4261 Dihedral : 15.024 179.708 4199 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.56 % Allowed : 14.04 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.15), residues: 2949 helix: 1.04 (0.17), residues: 926 sheet: -0.17 (0.23), residues: 494 loop : -2.08 (0.15), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 185 TYR 0.014 0.001 TYR C 97 PHE 0.016 0.001 PHE C 44 TRP 0.011 0.001 TRP I 49 HIS 0.009 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00282 (24807) covalent geometry : angle 0.52888 (33959) hydrogen bonds : bond 0.03031 ( 995) hydrogen bonds : angle 4.53866 ( 2830) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 260 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: A 10 TRP cc_start: 0.5681 (OUTLIER) cc_final: 0.4674 (p-90) REVERT: A 62 GLN cc_start: 0.7735 (mp10) cc_final: 0.7397 (mp10) REVERT: A 200 HIS cc_start: 0.8418 (t-90) cc_final: 0.7827 (t-90) REVERT: A 228 TRP cc_start: 0.7686 (t-100) cc_final: 0.7282 (t-100) REVERT: A 235 TYR cc_start: 0.8129 (m-80) cc_final: 0.7641 (m-80) REVERT: A 257 GLU cc_start: 0.7973 (mp0) cc_final: 0.7292 (mp0) REVERT: A 433 ARG cc_start: 0.5321 (ptt-90) cc_final: 0.4465 (ptp90) REVERT: B 189 ARG cc_start: 0.8289 (mtp85) cc_final: 0.7983 (mtp85) REVERT: B 268 ARG cc_start: 0.7553 (tpt170) cc_final: 0.7249 (ttt90) REVERT: C 19 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8321 (tt0) REVERT: C 143 PHE cc_start: 0.6895 (p90) cc_final: 0.6079 (p90) REVERT: D 212 ASP cc_start: 0.8137 (m-30) cc_final: 0.7833 (m-30) REVERT: E 318 LYS cc_start: 0.8830 (ptmt) cc_final: 0.8268 (pttp) REVERT: F 188 GLU cc_start: 0.8306 (pm20) cc_final: 0.7857 (pm20) REVERT: F 258 LYS cc_start: 0.7189 (mmpt) cc_final: 0.6970 (mmpt) REVERT: F 269 ARG cc_start: 0.8284 (ptp-170) cc_final: 0.8077 (mtm180) REVERT: G 206 LYS cc_start: 0.8385 (mmmt) cc_final: 0.7950 (mtmt) REVERT: H 72 ILE cc_start: 0.8999 (tp) cc_final: 0.8786 (tp) REVERT: H 74 ASN cc_start: 0.8705 (p0) cc_final: 0.8492 (p0) REVERT: H 94 ASN cc_start: 0.8431 (p0) cc_final: 0.7325 (t0) REVERT: I 34 GLU cc_start: 0.8800 (tt0) cc_final: 0.8418 (tt0) REVERT: J 90 ASN cc_start: 0.8308 (t0) cc_final: 0.7908 (t0) REVERT: J 99 HIS cc_start: 0.8274 (OUTLIER) cc_final: 0.7565 (p-80) REVERT: K 82 LYS cc_start: 0.8887 (ttmt) cc_final: 0.8368 (tttm) REVERT: K 90 ASN cc_start: 0.8784 (t0) cc_final: 0.8386 (t0) REVERT: K 99 HIS cc_start: 0.8280 (OUTLIER) cc_final: 0.5855 (p-80) outliers start: 59 outliers final: 39 residues processed: 296 average time/residue: 0.1786 time to fit residues: 79.5764 Evaluate side-chains 279 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 236 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 414 TRP Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 237 ARG Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 304 TYR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 304 TYR Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 94 ASN Chi-restraints excluded: chain I residue 333 ARG Chi-restraints excluded: chain J residue 99 HIS Chi-restraints excluded: chain K residue 99 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 32 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 142 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 166 optimal weight: 0.5980 chunk 30 optimal weight: 6.9990 chunk 283 optimal weight: 5.9990 chunk 197 optimal weight: 4.9990 chunk 146 optimal weight: 0.0040 chunk 14 optimal weight: 20.0000 chunk 141 optimal weight: 0.6980 overall best weight: 1.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS ** C 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 129 ASN I 159 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.138682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.095556 restraints weight = 34252.283| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.18 r_work: 0.2781 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24807 Z= 0.148 Angle : 0.535 7.549 33959 Z= 0.278 Chirality : 0.040 0.267 3815 Planarity : 0.004 0.049 4261 Dihedral : 14.961 179.603 4199 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.61 % Allowed : 15.12 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.15), residues: 2949 helix: 1.27 (0.17), residues: 922 sheet: -0.08 (0.23), residues: 489 loop : -2.02 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 278 TYR 0.011 0.001 TYR E 290 PHE 0.014 0.001 PHE C 44 TRP 0.012 0.001 TRP I 49 HIS 0.010 0.001 HIS C 29 Details of bonding type rmsd covalent geometry : bond 0.00334 (24807) covalent geometry : angle 0.53545 (33959) hydrogen bonds : bond 0.03024 ( 995) hydrogen bonds : angle 4.48692 ( 2830) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 250 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 TRP cc_start: 0.5651 (OUTLIER) cc_final: 0.4720 (p-90) REVERT: A 62 GLN cc_start: 0.7747 (mp10) cc_final: 0.7401 (mp10) REVERT: A 200 HIS cc_start: 0.8419 (t-90) cc_final: 0.7904 (t-90) REVERT: A 228 TRP cc_start: 0.7690 (t-100) cc_final: 0.7365 (t-100) REVERT: A 235 TYR cc_start: 0.8136 (m-80) cc_final: 0.7671 (m-80) REVERT: A 257 GLU cc_start: 0.7835 (mp0) cc_final: 0.7212 (mp0) REVERT: A 433 ARG cc_start: 0.5295 (ptt-90) cc_final: 0.4538 (ptp90) REVERT: B 268 ARG cc_start: 0.7604 (tpt170) cc_final: 0.7294 (ttt90) REVERT: C 143 PHE cc_start: 0.6897 (p90) cc_final: 0.6066 (p90) REVERT: D 212 ASP cc_start: 0.8159 (m-30) cc_final: 0.7835 (m-30) REVERT: D 304 TYR cc_start: 0.8666 (OUTLIER) cc_final: 0.8316 (m-80) REVERT: E 318 LYS cc_start: 0.8819 (ptmt) cc_final: 0.8254 (pttp) REVERT: F 77 LYS cc_start: 0.8348 (mtmt) cc_final: 0.8045 (mtpt) REVERT: F 188 GLU cc_start: 0.8330 (pm20) cc_final: 0.8048 (mp0) REVERT: G 185 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8164 (mmt-90) REVERT: G 206 LYS cc_start: 0.8439 (mmmt) cc_final: 0.7959 (mtmt) REVERT: H 72 ILE cc_start: 0.9100 (tp) cc_final: 0.8894 (tp) REVERT: H 74 ASN cc_start: 0.8662 (p0) cc_final: 0.8439 (p0) REVERT: H 94 ASN cc_start: 0.8446 (p0) cc_final: 0.8180 (p0) REVERT: H 310 GLN cc_start: 0.8574 (tt0) cc_final: 0.8314 (mt0) REVERT: I 34 GLU cc_start: 0.8782 (tt0) cc_final: 0.8399 (tt0) REVERT: J 90 ASN cc_start: 0.8346 (t0) cc_final: 0.7943 (t0) REVERT: J 99 HIS cc_start: 0.8311 (OUTLIER) cc_final: 0.7672 (p-80) REVERT: K 82 LYS cc_start: 0.8935 (ttmt) cc_final: 0.8395 (tttm) REVERT: K 90 ASN cc_start: 0.8783 (t0) cc_final: 0.8466 (t0) REVERT: K 99 HIS cc_start: 0.8269 (OUTLIER) cc_final: 0.5910 (p-80) outliers start: 60 outliers final: 37 residues processed: 290 average time/residue: 0.1876 time to fit residues: 81.7872 Evaluate side-chains 279 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 237 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 185 ARG Chi-restraints excluded: chain G residue 237 ARG Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 304 TYR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 304 TYR Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 94 ASN Chi-restraints excluded: chain I residue 333 ARG Chi-restraints excluded: chain J residue 99 HIS Chi-restraints excluded: chain K residue 99 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 33 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 290 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 173 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 12 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN A 203 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN C 153 GLN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 GLN F 159 HIS G 163 ASN ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.135146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.091802 restraints weight = 43084.930| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.94 r_work: 0.2641 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 24807 Z= 0.256 Angle : 0.608 8.958 33959 Z= 0.314 Chirality : 0.042 0.183 3815 Planarity : 0.004 0.052 4261 Dihedral : 14.998 178.933 4199 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.74 % Allowed : 16.25 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.15), residues: 2949 helix: 1.13 (0.17), residues: 927 sheet: -0.23 (0.22), residues: 520 loop : -2.05 (0.15), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 117 TYR 0.016 0.002 TYR G 324 PHE 0.012 0.001 PHE F 114 TRP 0.020 0.001 TRP E 49 HIS 0.010 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00586 (24807) covalent geometry : angle 0.60763 (33959) hydrogen bonds : bond 0.03370 ( 995) hydrogen bonds : angle 4.64792 ( 2830) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 242 time to evaluate : 0.945 Fit side-chains REVERT: A 10 TRP cc_start: 0.5644 (OUTLIER) cc_final: 0.4779 (p-90) REVERT: A 62 GLN cc_start: 0.7706 (mp10) cc_final: 0.7341 (mp10) REVERT: A 200 HIS cc_start: 0.8372 (t-90) cc_final: 0.7785 (t-90) REVERT: A 228 TRP cc_start: 0.7685 (t-100) cc_final: 0.7364 (t-100) REVERT: A 235 TYR cc_start: 0.8171 (m-80) cc_final: 0.7814 (m-80) REVERT: A 257 GLU cc_start: 0.7807 (mp0) cc_final: 0.7277 (mp0) REVERT: A 433 ARG cc_start: 0.5270 (ptt-90) cc_final: 0.4502 (ptp90) REVERT: B 218 ARG cc_start: 0.7277 (ptt180) cc_final: 0.7011 (ptt-90) REVERT: B 268 ARG cc_start: 0.7539 (tpt170) cc_final: 0.7217 (ttt90) REVERT: C 56 GLU cc_start: 0.7446 (pm20) cc_final: 0.6639 (pt0) REVERT: C 143 PHE cc_start: 0.6841 (p90) cc_final: 0.5976 (p90) REVERT: D 146 ASN cc_start: 0.8786 (t0) cc_final: 0.8418 (t0) REVERT: D 212 ASP cc_start: 0.8091 (m-30) cc_final: 0.7745 (m-30) REVERT: D 304 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.8247 (m-80) REVERT: E 318 LYS cc_start: 0.8846 (ptmt) cc_final: 0.8216 (pttp) REVERT: F 188 GLU cc_start: 0.8343 (pm20) cc_final: 0.8059 (mp0) REVERT: G 206 LYS cc_start: 0.8352 (mmmt) cc_final: 0.7874 (mtmt) REVERT: H 34 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8672 (mm-30) REVERT: H 94 ASN cc_start: 0.8313 (p0) cc_final: 0.7393 (t0) REVERT: H 310 GLN cc_start: 0.8558 (tt0) cc_final: 0.8258 (mt0) REVERT: I 34 GLU cc_start: 0.8690 (tt0) cc_final: 0.8246 (tt0) REVERT: J 90 ASN cc_start: 0.8379 (t0) cc_final: 0.7928 (t0) REVERT: J 99 HIS cc_start: 0.8248 (OUTLIER) cc_final: 0.7794 (p-80) REVERT: K 82 LYS cc_start: 0.8915 (ttmt) cc_final: 0.8336 (ttmt) REVERT: K 90 ASN cc_start: 0.8746 (t0) cc_final: 0.8363 (t0) REVERT: K 99 HIS cc_start: 0.8366 (OUTLIER) cc_final: 0.6089 (p-80) outliers start: 63 outliers final: 46 residues processed: 281 average time/residue: 0.1966 time to fit residues: 82.9639 Evaluate side-chains 279 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 229 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 203 ARG Chi-restraints excluded: chain G residue 237 ARG Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 304 TYR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 304 TYR Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 94 ASN Chi-restraints excluded: chain J residue 99 HIS Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 117 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 227 optimal weight: 0.9990 chunk 37 optimal weight: 20.0000 chunk 260 optimal weight: 0.9990 chunk 228 optimal weight: 0.9980 chunk 36 optimal weight: 0.0270 chunk 230 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 206 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 283 optimal weight: 1.9990 overall best weight: 0.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS ** C 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 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 = 0.3661 r_free = 0.3661 target = 0.139222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.096187 restraints weight = 35551.475| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.23 r_work: 0.2800 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24807 Z= 0.120 Angle : 0.526 8.262 33959 Z= 0.273 Chirality : 0.039 0.170 3815 Planarity : 0.004 0.053 4261 Dihedral : 14.889 178.979 4199 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.26 % Allowed : 16.99 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.15), residues: 2949 helix: 1.46 (0.17), residues: 921 sheet: -0.12 (0.22), residues: 500 loop : -1.96 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 185 TYR 0.013 0.001 TYR F 290 PHE 0.010 0.001 PHE C 44 TRP 0.013 0.001 TRP I 49 HIS 0.010 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00265 (24807) covalent geometry : angle 0.52606 (33959) hydrogen bonds : bond 0.02872 ( 995) hydrogen bonds : angle 4.42451 ( 2830) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 259 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 10 TRP cc_start: 0.5599 (OUTLIER) cc_final: 0.4746 (p-90) REVERT: A 28 LYS cc_start: 0.8009 (mtpp) cc_final: 0.7708 (pttt) REVERT: A 62 GLN cc_start: 0.7645 (mp10) cc_final: 0.7336 (mp10) REVERT: A 200 HIS cc_start: 0.8395 (t-90) cc_final: 0.7801 (t-90) REVERT: A 228 TRP cc_start: 0.7559 (t-100) cc_final: 0.7168 (t-100) REVERT: A 235 TYR cc_start: 0.8165 (m-80) cc_final: 0.7857 (m-80) REVERT: A 257 GLU cc_start: 0.7805 (mp0) cc_final: 0.7240 (mp0) REVERT: A 433 ARG cc_start: 0.5288 (ptt-90) cc_final: 0.4523 (ptp90) REVERT: B 170 ARG cc_start: 0.8454 (tmm-80) cc_final: 0.7564 (mtm110) REVERT: B 189 ARG cc_start: 0.8319 (mtp85) cc_final: 0.8002 (mtp85) REVERT: C 143 PHE cc_start: 0.6844 (p90) cc_final: 0.6000 (p90) REVERT: C 186 TRP cc_start: 0.7443 (t-100) cc_final: 0.6953 (t-100) REVERT: D 146 ASN cc_start: 0.8764 (t0) cc_final: 0.8373 (t0) REVERT: D 212 ASP cc_start: 0.8121 (m-30) cc_final: 0.7734 (m-30) REVERT: D 304 TYR cc_start: 0.8759 (OUTLIER) cc_final: 0.8387 (m-80) REVERT: F 188 GLU cc_start: 0.8378 (pm20) cc_final: 0.8108 (mp0) REVERT: G 185 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8054 (mmt-90) REVERT: G 206 LYS cc_start: 0.8475 (mmmt) cc_final: 0.8048 (mtmt) REVERT: H 94 ASN cc_start: 0.8418 (p0) cc_final: 0.7339 (t0) REVERT: H 310 GLN cc_start: 0.8636 (tt0) cc_final: 0.8369 (mt0) REVERT: I 34 GLU cc_start: 0.8819 (tt0) cc_final: 0.8408 (tt0) REVERT: J 90 ASN cc_start: 0.8373 (t0) cc_final: 0.7967 (t0) REVERT: J 99 HIS cc_start: 0.8338 (OUTLIER) cc_final: 0.7665 (p-80) REVERT: K 82 LYS cc_start: 0.9034 (ttmt) cc_final: 0.8477 (tttm) REVERT: K 90 ASN cc_start: 0.8854 (t0) cc_final: 0.8550 (t0) REVERT: K 99 HIS cc_start: 0.8304 (OUTLIER) cc_final: 0.6088 (p-80) outliers start: 52 outliers final: 38 residues processed: 291 average time/residue: 0.1975 time to fit residues: 86.0288 Evaluate side-chains 280 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 237 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 146 ASN Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 185 ARG Chi-restraints excluded: chain G residue 237 ARG Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 304 TYR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 304 TYR Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 94 ASN Chi-restraints excluded: chain J residue 99 HIS Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 99 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 283 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 235 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 164 optimal weight: 4.9990 chunk 13 optimal weight: 20.0000 chunk 135 optimal weight: 0.0570 chunk 27 optimal weight: 0.0070 chunk 225 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 overall best weight: 0.9718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS ** C 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN E 148 GLN ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.138891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.095815 restraints weight = 36136.471| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.22 r_work: 0.2825 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24807 Z= 0.130 Angle : 0.531 8.811 33959 Z= 0.274 Chirality : 0.040 0.351 3815 Planarity : 0.004 0.051 4261 Dihedral : 14.796 179.696 4199 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.17 % Allowed : 17.21 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.15), residues: 2949 helix: 1.59 (0.17), residues: 922 sheet: -0.04 (0.23), residues: 500 loop : -1.92 (0.15), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 185 TYR 0.017 0.001 TYR I 304 PHE 0.008 0.001 PHE B 40 TRP 0.014 0.001 TRP A 394 HIS 0.009 0.001 HIS C 29 Details of bonding type rmsd covalent geometry : bond 0.00292 (24807) covalent geometry : angle 0.53103 (33959) hydrogen bonds : bond 0.02888 ( 995) hydrogen bonds : angle 4.38307 ( 2830) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 252 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: A 10 TRP cc_start: 0.5560 (OUTLIER) cc_final: 0.4772 (p-90) REVERT: A 28 LYS cc_start: 0.7977 (mtpp) cc_final: 0.7671 (pttt) REVERT: A 62 GLN cc_start: 0.7659 (mp10) cc_final: 0.7344 (mp10) REVERT: A 200 HIS cc_start: 0.8410 (t-90) cc_final: 0.7868 (t-90) REVERT: A 228 TRP cc_start: 0.7578 (t-100) cc_final: 0.7161 (t-100) REVERT: A 235 TYR cc_start: 0.8158 (m-80) cc_final: 0.7805 (m-80) REVERT: A 257 GLU cc_start: 0.7772 (mp0) cc_final: 0.7196 (mp0) REVERT: A 433 ARG cc_start: 0.5271 (ptt-90) cc_final: 0.4507 (ptp90) REVERT: B 189 ARG cc_start: 0.8312 (mtp85) cc_final: 0.8013 (mtp85) REVERT: C 143 PHE cc_start: 0.6934 (p90) cc_final: 0.6051 (p90) REVERT: C 186 TRP cc_start: 0.7443 (t-100) cc_final: 0.6981 (t-100) REVERT: D 146 ASN cc_start: 0.8772 (t0) cc_final: 0.8401 (t0) REVERT: D 212 ASP cc_start: 0.8103 (m-30) cc_final: 0.7712 (m-30) REVERT: D 304 TYR cc_start: 0.8710 (OUTLIER) cc_final: 0.8223 (m-80) REVERT: E 130 ASP cc_start: 0.8403 (m-30) cc_final: 0.8051 (t0) REVERT: E 318 LYS cc_start: 0.8895 (ptmt) cc_final: 0.8261 (pttp) REVERT: F 188 GLU cc_start: 0.8301 (pm20) cc_final: 0.8042 (mp0) REVERT: F 206 LYS cc_start: 0.8790 (mtmm) cc_final: 0.8499 (mmtt) REVERT: G 105 SER cc_start: 0.9263 (m) cc_final: 0.9009 (p) REVERT: G 185 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8113 (mmt-90) REVERT: G 206 LYS cc_start: 0.8461 (mmmt) cc_final: 0.8047 (mtmt) REVERT: H 94 ASN cc_start: 0.8410 (p0) cc_final: 0.8162 (p0) REVERT: H 310 GLN cc_start: 0.8614 (tt0) cc_final: 0.8366 (mt0) REVERT: J 90 ASN cc_start: 0.8506 (t0) cc_final: 0.8127 (t0) REVERT: J 99 HIS cc_start: 0.8332 (OUTLIER) cc_final: 0.7703 (p-80) REVERT: K 82 LYS cc_start: 0.9031 (ttmt) cc_final: 0.8507 (ttmt) REVERT: K 90 ASN cc_start: 0.8847 (t0) cc_final: 0.8567 (t0) REVERT: K 99 HIS cc_start: 0.8352 (OUTLIER) cc_final: 0.6105 (p-80) outliers start: 50 outliers final: 37 residues processed: 284 average time/residue: 0.1941 time to fit residues: 83.0051 Evaluate side-chains 279 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 237 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 146 ASN Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 185 ARG Chi-restraints excluded: chain G residue 237 ARG Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 304 TYR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 304 TYR Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 94 ASN Chi-restraints excluded: chain J residue 99 HIS Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 99 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 118 optimal weight: 0.9980 chunk 291 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 235 optimal weight: 0.0570 chunk 14 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 overall best weight: 2.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 HIS ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS ** C 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN C 153 GLN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN G 94 ASN G 260 GLN ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.135217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.092234 restraints weight = 33713.778| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.10 r_work: 0.2750 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2525 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2525 r_free = 0.2525 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2525 r_free = 0.2525 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 24807 Z= 0.222 Angle : 0.594 9.139 33959 Z= 0.306 Chirality : 0.042 0.179 3815 Planarity : 0.004 0.050 4261 Dihedral : 14.870 179.683 4199 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.26 % Allowed : 17.64 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.15), residues: 2949 helix: 1.44 (0.17), residues: 916 sheet: -0.10 (0.22), residues: 520 loop : -1.98 (0.15), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 237 TYR 0.016 0.002 TYR G 324 PHE 0.014 0.001 PHE C 44 TRP 0.018 0.001 TRP E 49 HIS 0.011 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00510 (24807) covalent geometry : angle 0.59404 (33959) hydrogen bonds : bond 0.03250 ( 995) hydrogen bonds : angle 4.53793 ( 2830) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 237 time to evaluate : 0.921 Fit side-chains REVERT: A 10 TRP cc_start: 0.5628 (OUTLIER) cc_final: 0.4844 (p-90) REVERT: A 28 LYS cc_start: 0.8022 (mtpp) cc_final: 0.7767 (pttt) REVERT: A 62 GLN cc_start: 0.7629 (mp10) cc_final: 0.7291 (mp10) REVERT: A 200 HIS cc_start: 0.8462 (t-90) cc_final: 0.7846 (t-90) REVERT: A 228 TRP cc_start: 0.7572 (t-100) cc_final: 0.7202 (t-100) REVERT: A 235 TYR cc_start: 0.8211 (m-80) cc_final: 0.7848 (m-80) REVERT: A 257 GLU cc_start: 0.7800 (mp0) cc_final: 0.7301 (mp0) REVERT: A 433 ARG cc_start: 0.5288 (ptt-90) cc_final: 0.4513 (ptp90) REVERT: B 89 ASN cc_start: 0.8970 (m-40) cc_final: 0.8643 (m110) REVERT: B 147 TRP cc_start: 0.8411 (t-100) cc_final: 0.8102 (t-100) REVERT: B 218 ARG cc_start: 0.7277 (ptt180) cc_final: 0.7058 (ptt-90) REVERT: C 56 GLU cc_start: 0.7973 (pm20) cc_final: 0.7441 (pm20) REVERT: C 143 PHE cc_start: 0.6959 (p90) cc_final: 0.6099 (p90) REVERT: D 146 ASN cc_start: 0.8846 (t0) cc_final: 0.8531 (t0) REVERT: D 212 ASP cc_start: 0.8129 (m-30) cc_final: 0.7804 (m-30) REVERT: D 304 TYR cc_start: 0.8825 (OUTLIER) cc_final: 0.8318 (m-80) REVERT: E 318 LYS cc_start: 0.8851 (ptmt) cc_final: 0.8341 (pttm) REVERT: F 188 GLU cc_start: 0.8475 (pm20) cc_final: 0.8237 (mp0) REVERT: F 206 LYS cc_start: 0.8770 (mtmm) cc_final: 0.8468 (mmtt) REVERT: G 206 LYS cc_start: 0.8421 (mmmt) cc_final: 0.7977 (mtmt) REVERT: H 94 ASN cc_start: 0.8402 (p0) cc_final: 0.8140 (p0) REVERT: H 310 GLN cc_start: 0.8666 (tt0) cc_final: 0.8401 (mt0) REVERT: I 34 GLU cc_start: 0.8777 (tt0) cc_final: 0.8395 (tt0) REVERT: I 302 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8419 (mt-10) REVERT: J 90 ASN cc_start: 0.8478 (t0) cc_final: 0.8053 (t0) REVERT: K 82 LYS cc_start: 0.9040 (ttmt) cc_final: 0.8448 (ttmt) REVERT: K 90 ASN cc_start: 0.8810 (t0) cc_final: 0.8454 (t0) REVERT: K 99 HIS cc_start: 0.8397 (OUTLIER) cc_final: 0.6165 (p-80) outliers start: 52 outliers final: 37 residues processed: 271 average time/residue: 0.1983 time to fit residues: 81.2081 Evaluate side-chains 273 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 232 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 203 ARG Chi-restraints excluded: chain G residue 237 ARG Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 304 TYR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 304 TYR Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 94 ASN Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain K residue 99 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 120 optimal weight: 1.9990 chunk 267 optimal weight: 3.9990 chunk 240 optimal weight: 0.0770 chunk 249 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 270 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 15 optimal weight: 0.0270 chunk 230 optimal weight: 0.2980 chunk 104 optimal weight: 4.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS ** C 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 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 = 0.3664 r_free = 0.3664 target = 0.139463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.097727 restraints weight = 44474.166| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.61 r_work: 0.2810 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24807 Z= 0.104 Angle : 0.523 9.219 33959 Z= 0.271 Chirality : 0.039 0.167 3815 Planarity : 0.004 0.051 4261 Dihedral : 14.737 178.508 4199 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.78 % Allowed : 17.99 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.15), residues: 2949 helix: 1.67 (0.17), residues: 922 sheet: 0.12 (0.23), residues: 473 loop : -1.85 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 237 TYR 0.010 0.001 TYR I 304 PHE 0.011 0.001 PHE C 44 TRP 0.013 0.001 TRP A 394 HIS 0.009 0.001 HIS C 29 Details of bonding type rmsd covalent geometry : bond 0.00229 (24807) covalent geometry : angle 0.52342 (33959) hydrogen bonds : bond 0.02814 ( 995) hydrogen bonds : angle 4.31582 ( 2830) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 253 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 TRP cc_start: 0.5488 (OUTLIER) cc_final: 0.4679 (p-90) REVERT: A 28 LYS cc_start: 0.7983 (mtpp) cc_final: 0.7736 (pttt) REVERT: A 62 GLN cc_start: 0.7639 (mp10) cc_final: 0.7309 (mp10) REVERT: A 200 HIS cc_start: 0.8285 (t-90) cc_final: 0.7761 (t-90) REVERT: A 228 TRP cc_start: 0.7399 (t-100) cc_final: 0.6980 (t-100) REVERT: A 235 TYR cc_start: 0.8106 (m-80) cc_final: 0.7856 (m-80) REVERT: A 257 GLU cc_start: 0.7739 (mp0) cc_final: 0.7180 (mp0) REVERT: A 433 ARG cc_start: 0.5264 (ptt-90) cc_final: 0.4517 (ptp90) REVERT: B 89 ASN cc_start: 0.8899 (m-40) cc_final: 0.8632 (m110) REVERT: B 189 ARG cc_start: 0.8231 (mtp85) cc_final: 0.7942 (mtp85) REVERT: C 44 PHE cc_start: 0.8302 (m-80) cc_final: 0.7880 (m-10) REVERT: C 56 GLU cc_start: 0.7907 (pm20) cc_final: 0.7377 (pm20) REVERT: C 143 PHE cc_start: 0.6834 (p90) cc_final: 0.5980 (p90) REVERT: C 186 TRP cc_start: 0.7395 (t-100) cc_final: 0.6881 (t-100) REVERT: D 146 ASN cc_start: 0.8695 (t0) cc_final: 0.8319 (t0) REVERT: D 212 ASP cc_start: 0.7898 (m-30) cc_final: 0.7557 (m-30) REVERT: D 304 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.8188 (m-80) REVERT: E 130 ASP cc_start: 0.8278 (m-30) cc_final: 0.7964 (t0) REVERT: F 188 GLU cc_start: 0.8170 (pm20) cc_final: 0.7958 (mp0) REVERT: F 206 LYS cc_start: 0.8763 (mtmm) cc_final: 0.8531 (mmtt) REVERT: G 105 SER cc_start: 0.9151 (m) cc_final: 0.8908 (p) REVERT: G 185 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7970 (mmt-90) REVERT: G 206 LYS cc_start: 0.8417 (mmmt) cc_final: 0.8079 (mtmt) REVERT: H 69 ARG cc_start: 0.8744 (mmm-85) cc_final: 0.8192 (ttt180) REVERT: H 94 ASN cc_start: 0.8336 (p0) cc_final: 0.8044 (p0) REVERT: H 310 GLN cc_start: 0.8510 (tt0) cc_final: 0.8208 (mt0) REVERT: I 34 GLU cc_start: 0.8597 (tt0) cc_final: 0.8185 (tt0) REVERT: J 90 ASN cc_start: 0.8462 (t0) cc_final: 0.8079 (t0) REVERT: K 82 LYS cc_start: 0.9051 (ttmt) cc_final: 0.8488 (ttmt) REVERT: K 90 ASN cc_start: 0.8778 (t0) cc_final: 0.8482 (t0) REVERT: K 99 HIS cc_start: 0.8244 (OUTLIER) cc_final: 0.6119 (p-80) outliers start: 41 outliers final: 32 residues processed: 276 average time/residue: 0.2112 time to fit residues: 86.5095 Evaluate side-chains 280 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 244 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 185 ARG Chi-restraints excluded: chain G residue 237 ARG Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 304 TYR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 304 TYR Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 94 ASN Chi-restraints excluded: chain K residue 99 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 21 optimal weight: 20.0000 chunk 65 optimal weight: 7.9990 chunk 79 optimal weight: 0.1980 chunk 225 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 218 optimal weight: 0.0980 chunk 182 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.0010 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS ** C 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN ** E 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.139521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.097602 restraints weight = 36219.934| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.15 r_work: 0.2821 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24807 Z= 0.119 Angle : 0.528 9.089 33959 Z= 0.272 Chirality : 0.039 0.172 3815 Planarity : 0.004 0.050 4261 Dihedral : 14.690 179.301 4199 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.78 % Allowed : 18.17 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.15), residues: 2949 helix: 1.80 (0.17), residues: 914 sheet: 0.13 (0.23), residues: 477 loop : -1.80 (0.15), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 333 TYR 0.011 0.001 TYR E 290 PHE 0.013 0.001 PHE C 44 TRP 0.021 0.001 TRP A 394 HIS 0.013 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00267 (24807) covalent geometry : angle 0.52775 (33959) hydrogen bonds : bond 0.02929 ( 995) hydrogen bonds : angle 4.28720 ( 2830) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6628.23 seconds wall clock time: 114 minutes 2.26 seconds (6842.26 seconds total)