Starting phenix.real_space_refine on Sat Jul 4 23:50:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jzz_22585/07_2026/7jzz_22585.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jzz_22585/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7jzz_22585/07_2026/7jzz_22585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jzz_22585/07_2026/7jzz_22585.map" model { file = "/net/cci-nas-00/data/ceres_data/7jzz_22585/07_2026/7jzz_22585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jzz_22585/07_2026/7jzz_22585.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7jzz_22585/07_2026/7jzz_22585.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jzz_22585/07_2026/7jzz_22585.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 12 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: 5.12, per 1000 atoms: 0.21 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: 1.96 Conformation dependent library (CDL) restraints added in 1.6 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: 3.23 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: 5.08 Time building geometry restraints manager: 2.65 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: 14375 35.93 - 71.86: 360 71.86 - 107.79: 17 107.79 - 143.72: 3 143.72 - 179.65: 4 Dihedral angle restraints: 14759 sinusoidal: 6185 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 14756 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: 1.200 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: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 26.020 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 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 : 16.104 179.653 9225 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/Z covalent geometry : bond 0.01049 / 0.46 (24807) covalent geometry : angle 0.97716 / 0.55 (33959) hydrogen bonds : bond 0.16789 / 11.12 ( 995) hydrogen bonds : angle 7.39777 / 5.17 ( 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 : 0.740 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: 0.2243 time to fit residues: 110.0087 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 : 0.874 ------------------------------------------------------------------------------- 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... 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 = 0.3650 r_free = 0.3650 target = 0.138279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.095561 restraints weight = 33762.866| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.11 r_work: 0.2767 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2590 r_free = 0.2590 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 = 0.2590 r_free = 0.2590 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24807 Z= 0.133 Angle : 0.584 9.224 33959 Z= 0.306 Chirality : 0.040 0.187 3815 Planarity : 0.005 0.059 4261 Dihedral : 12.109 179.260 3985 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.61 % Allowed : 11.95 % Favored : 86.44 % 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: -2.24 (0.14), residues: 2949 helix: -0.55 (0.15), residues: 925 sheet: -0.69 (0.22), residues: 492 loop : -2.43 (0.13), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 237 TYR 0.018 0.001 TYR C 97 PHE 0.021 0.001 PHE A 391 TRP 0.013 0.001 TRP G 49 HIS 0.006 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (24807) covalent geometry : angle 0.58354 / 0.31 (33959) hydrogen bonds : bond 0.03809 / 2.61 ( 995) hydrogen bonds : angle 5.19377 / 3.66 ( 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: 37 poor density : 279 time to evaluate : 0.868 Fit side-chains REVERT: A 10 TRP cc_start: 0.5852 (OUTLIER) cc_final: 0.4490 (p-90) REVERT: A 62 GLN cc_start: 0.7805 (mp10) cc_final: 0.7513 (mp10) REVERT: A 200 HIS cc_start: 0.8392 (t-90) cc_final: 0.7812 (t-90) REVERT: A 235 TYR cc_start: 0.8202 (m-80) cc_final: 0.7737 (m-80) REVERT: B 189 ARG cc_start: 0.8211 (mtp85) cc_final: 0.7902 (mtp85) REVERT: B 218 ARG cc_start: 0.7456 (ptt180) cc_final: 0.6933 (ptt-90) REVERT: B 268 ARG cc_start: 0.7580 (tpt170) cc_final: 0.7171 (ttt90) REVERT: C 44 PHE cc_start: 0.8565 (m-80) cc_final: 0.8301 (m-10) REVERT: C 84 GLN cc_start: 0.7754 (pt0) cc_final: 0.7480 (pt0) REVERT: C 143 PHE cc_start: 0.7139 (p90) cc_final: 0.6226 (p90) REVERT: D 294 ASP cc_start: 0.7934 (t0) cc_final: 0.7616 (t0) REVERT: F 51 GLN cc_start: 0.8216 (pt0) cc_final: 0.7993 (pt0) REVERT: F 77 LYS cc_start: 0.8224 (mtpt) cc_final: 0.8023 (mtmt) REVERT: F 188 GLU cc_start: 0.8455 (pm20) cc_final: 0.8164 (pm20) REVERT: G 188 GLU cc_start: 0.8053 (mp0) cc_final: 0.7790 (mm-30) REVERT: G 206 LYS cc_start: 0.8374 (mmmt) cc_final: 0.7815 (mtmt) REVERT: H 72 ILE cc_start: 0.9035 (tp) cc_final: 0.8766 (tp) REVERT: H 94 ASN cc_start: 0.8420 (p0) cc_final: 0.7586 (t0) REVERT: I 34 GLU cc_start: 0.8884 (tt0) cc_final: 0.8660 (tt0) REVERT: I 73 SER cc_start: 0.9124 (m) cc_final: 0.8532 (p) REVERT: I 185 ARG cc_start: 0.7796 (tpp80) cc_final: 0.7413 (tpp-160) REVERT: I 254 LYS cc_start: 0.7847 (mmtt) cc_final: 0.7327 (mppt) REVERT: I 261 LYS cc_start: 0.8022 (mttt) cc_final: 0.7819 (mttt) REVERT: J 90 ASN cc_start: 0.8350 (t0) cc_final: 0.7919 (t0) REVERT: J 99 HIS cc_start: 0.8198 (OUTLIER) cc_final: 0.7582 (p-80) REVERT: J 110 GLN cc_start: 0.8503 (tp40) cc_final: 0.8297 (tp40) REVERT: J 114 ASN cc_start: 0.8213 (m-40) cc_final: 0.7987 (m-40) REVERT: K 82 LYS cc_start: 0.8726 (ttmt) cc_final: 0.8437 (tttm) REVERT: K 90 ASN cc_start: 0.8568 (t0) cc_final: 0.8105 (t0) REVERT: K 99 HIS cc_start: 0.8107 (OUTLIER) cc_final: 0.5906 (p-80) outliers start: 37 outliers final: 18 residues processed: 305 average time/residue: 0.2043 time to fit residues: 93.3878 Evaluate side-chains 266 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 245 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP 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 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: 0.9980 chunk 87 optimal weight: 5.9990 chunk 56 optimal weight: 0.0070 chunk 138 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 chunk 252 optimal weight: 5.9990 chunk 256 optimal weight: 0.4980 chunk 124 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 ASN ** I 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.138830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.095504 restraints weight = 36404.053| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.27 r_work: 0.2764 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2577 r_free = 0.2577 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 = 0.2577 r_free = 0.2577 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24807 Z= 0.127 Angle : 0.543 8.102 33959 Z= 0.283 Chirality : 0.040 0.181 3815 Planarity : 0.004 0.050 4261 Dihedral : 11.835 179.363 3983 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.09 % Allowed : 13.12 % Favored : 84.79 % 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: -1.49 (0.14), residues: 2949 helix: 0.50 (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 0.005 0.000 ARG F 237 TYR 0.012 0.001 TYR F 290 PHE 0.015 0.001 PHE B 184 TRP 0.014 0.001 TRP A 394 HIS 0.009 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (24807) covalent geometry : angle 0.54280 / 0.28 (33959) hydrogen bonds : bond 0.03274 / 2.26 ( 995) hydrogen bonds : angle 4.78050 / 3.37 ( 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 307 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 259 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 62 GLN cc_start: 0.7784 (mp10) cc_final: 0.7435 (mp10) REVERT: A 200 HIS cc_start: 0.8436 (t-90) cc_final: 0.7919 (t-90) REVERT: A 228 TRP cc_start: 0.7717 (t-100) cc_final: 0.7300 (t-100) REVERT: A 235 TYR cc_start: 0.8154 (m-80) cc_final: 0.7690 (m-80) REVERT: A 257 GLU cc_start: 0.8006 (mp0) cc_final: 0.7373 (mp0) REVERT: B 184 PHE cc_start: 0.8687 (m-80) cc_final: 0.8450 (m-80) REVERT: B 189 ARG cc_start: 0.8244 (mtp85) cc_final: 0.7921 (mtp85) REVERT: B 268 ARG cc_start: 0.7582 (tpt170) cc_final: 0.7229 (ttt90) REVERT: B 306 HIS cc_start: 0.7887 (m-70) cc_final: 0.7654 (m-70) REVERT: C 143 PHE cc_start: 0.6982 (p90) cc_final: 0.6084 (p90) REVERT: D 212 ASP cc_start: 0.8072 (m-30) cc_final: 0.7826 (m-30) REVERT: D 294 ASP cc_start: 0.7853 (t0) cc_final: 0.7562 (t0) REVERT: F 102 ASN cc_start: 0.9304 (m-40) cc_final: 0.9008 (m110) REVERT: F 188 GLU cc_start: 0.8401 (pm20) cc_final: 0.7936 (pm20) REVERT: F 258 LYS cc_start: 0.7143 (mmpt) cc_final: 0.6780 (mmpt) REVERT: F 269 ARG cc_start: 0.8268 (ptp-170) cc_final: 0.7992 (mtm180) REVERT: G 69 ARG cc_start: 0.9225 (ttt180) cc_final: 0.9005 (ttt180) REVERT: G 188 GLU cc_start: 0.8104 (mp0) cc_final: 0.7852 (mm-30) REVERT: G 206 LYS cc_start: 0.8353 (mmmt) cc_final: 0.7889 (mtmt) REVERT: H 72 ILE cc_start: 0.9058 (tp) cc_final: 0.8830 (tp) REVERT: H 94 ASN cc_start: 0.8445 (p0) cc_final: 0.7604 (t0) REVERT: I 34 GLU cc_start: 0.8856 (tt0) cc_final: 0.8481 (tt0) REVERT: I 261 LYS cc_start: 0.8223 (mttt) cc_final: 0.7934 (mttt) REVERT: J 90 ASN cc_start: 0.8366 (t0) cc_final: 0.7955 (t0) REVERT: J 99 HIS cc_start: 0.8251 (OUTLIER) cc_final: 0.7474 (p-80) REVERT: J 110 GLN cc_start: 0.8595 (tp40) cc_final: 0.8393 (tp40) REVERT: J 114 ASN cc_start: 0.8257 (m-40) cc_final: 0.8018 (m-40) REVERT: K 82 LYS cc_start: 0.8795 (ttmt) cc_final: 0.8498 (tttm) REVERT: K 90 ASN cc_start: 0.8808 (t0) cc_final: 0.8332 (t0) REVERT: K 99 HIS cc_start: 0.8165 (OUTLIER) cc_final: 0.5706 (p-80) outliers start: 48 outliers final: 34 residues processed: 288 average time/residue: 0.1984 time to fit residues: 85.7255 Evaluate side-chains 265 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 229 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 F residue 143 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 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: 10.0000 chunk 188 optimal weight: 0.0000 chunk 95 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 279 optimal weight: 4.9990 chunk 192 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 154 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 201 optimal weight: 0.1980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 HIS ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 129 ASN 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 348 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.139044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.096003 restraints weight = 35611.010| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.26 r_work: 0.2776 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2582 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2582 r_free = 0.2582 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 = 0.2582 r_free = 0.2582 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2582 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2003 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= 0.131 Angle : 0.529 7.380 33959 Z= 0.274 Chirality : 0.039 0.181 3815 Planarity : 0.004 0.049 4261 Dihedral : 11.710 179.571 3983 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.56 % Allowed : 14.08 % Favored : 83.36 % 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: -1.07 (0.15), residues: 2949 helix: 1.01 (0.17), residues: 926 sheet: -0.19 (0.23), residues: 493 loop : -2.09 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 185 TYR 0.013 0.001 TYR C 97 PHE 0.013 0.001 PHE C 44 TRP 0.011 0.001 TRP I 49 HIS 0.014 0.001 HIS C 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (24807) covalent geometry : angle 0.52920 / 0.27 (33959) hydrogen bonds : bond 0.03064 / 2.12 ( 995) hydrogen bonds : angle 4.56254 / 3.21 ( 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 316 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 257 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 10 TRP cc_start: 0.5662 (OUTLIER) cc_final: 0.4638 (p-90) REVERT: A 62 GLN cc_start: 0.7736 (mp10) cc_final: 0.7396 (mp10) REVERT: A 200 HIS cc_start: 0.8413 (t-90) cc_final: 0.7821 (t-90) REVERT: A 228 TRP cc_start: 0.7692 (t-100) cc_final: 0.7330 (t-100) REVERT: A 235 TYR cc_start: 0.8126 (m-80) cc_final: 0.7638 (m-80) REVERT: A 257 GLU cc_start: 0.7975 (mp0) cc_final: 0.7307 (mp0) REVERT: B 189 ARG cc_start: 0.8225 (mtp85) cc_final: 0.7912 (mtp85) REVERT: B 268 ARG cc_start: 0.7520 (tpt170) cc_final: 0.7187 (ttt90) REVERT: C 143 PHE cc_start: 0.6885 (p90) cc_final: 0.6059 (p90) REVERT: D 212 ASP cc_start: 0.8115 (m-30) cc_final: 0.7813 (m-30) REVERT: E 318 LYS cc_start: 0.8825 (ptmt) cc_final: 0.8259 (pttp) REVERT: F 102 ASN cc_start: 0.9238 (m-40) cc_final: 0.8954 (m110) REVERT: F 188 GLU cc_start: 0.8304 (pm20) cc_final: 0.7843 (pm20) REVERT: F 258 LYS cc_start: 0.7206 (mmpt) cc_final: 0.6967 (mmpt) REVERT: F 269 ARG cc_start: 0.8283 (ptp-170) cc_final: 0.8064 (mtm180) REVERT: G 206 LYS cc_start: 0.8385 (mmmt) cc_final: 0.7928 (mtmt) REVERT: H 72 ILE cc_start: 0.9009 (tp) cc_final: 0.8788 (tp) REVERT: H 74 ASN cc_start: 0.8695 (p0) cc_final: 0.8471 (p0) REVERT: H 94 ASN cc_start: 0.8443 (p0) cc_final: 0.7343 (t0) REVERT: I 34 GLU cc_start: 0.8774 (tt0) cc_final: 0.8372 (tt0) REVERT: I 99 ASP cc_start: 0.8930 (m-30) cc_final: 0.8466 (m-30) REVERT: I 147 ASP cc_start: 0.8275 (t0) cc_final: 0.7951 (m-30) REVERT: I 261 LYS cc_start: 0.8235 (mttt) cc_final: 0.7733 (mttt) REVERT: J 90 ASN cc_start: 0.8290 (t0) cc_final: 0.7907 (t0) REVERT: J 99 HIS cc_start: 0.8263 (OUTLIER) cc_final: 0.7549 (p-80) REVERT: J 114 ASN cc_start: 0.8248 (m-40) cc_final: 0.8012 (m-40) REVERT: K 82 LYS cc_start: 0.8871 (ttmt) cc_final: 0.8333 (tttm) REVERT: K 90 ASN cc_start: 0.8759 (t0) cc_final: 0.8347 (t0) REVERT: K 99 HIS cc_start: 0.8278 (OUTLIER) cc_final: 0.5830 (p-80) outliers start: 59 outliers final: 38 residues processed: 296 average time/residue: 0.1941 time to fit residues: 86.8563 Evaluate side-chains 281 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 240 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 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 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 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 78 THR 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 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 71 THR Chi-restraints excluded: chain I residue 73 SER 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: 0.6980 chunk 169 optimal weight: 0.6980 chunk 142 optimal weight: 9.9990 chunk 161 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 283 optimal weight: 5.9990 chunk 197 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN F 148 GLN F 159 HIS G 51 GLN G 129 ASN G 163 ASN ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 129 ASN I 148 GLN I 159 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.133916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.091360 restraints weight = 33506.553| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.11 r_work: 0.2684 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2496 r_free = 0.2496 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2496 r_free = 0.2496 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 24807 Z= 0.266 Angle : 0.625 7.805 33959 Z= 0.322 Chirality : 0.043 0.185 3815 Planarity : 0.004 0.053 4261 Dihedral : 11.794 178.768 3983 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.13 % Allowed : 15.17 % Favored : 81.70 % 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: -1.10 (0.15), residues: 2949 helix: 1.01 (0.17), residues: 925 sheet: -0.28 (0.22), residues: 519 loop : -2.10 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 117 TYR 0.017 0.002 TYR G 324 PHE 0.015 0.002 PHE C 44 TRP 0.021 0.001 TRP E 49 HIS 0.012 0.001 HIS C 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.27 (24807) covalent geometry : angle 0.62456 / 0.32 (33959) hydrogen bonds : bond 0.03504 / 2.40 ( 995) hydrogen bonds : angle 4.73535 / 3.32 ( 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 318 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 246 time to evaluate : 0.946 Fit side-chains REVERT: A 10 TRP cc_start: 0.5794 (OUTLIER) cc_final: 0.4849 (p-90) REVERT: A 62 GLN cc_start: 0.7609 (mp10) cc_final: 0.7252 (mp10) REVERT: A 178 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8697 (mt) REVERT: A 200 HIS cc_start: 0.8487 (t-90) cc_final: 0.7928 (t-90) REVERT: A 228 TRP cc_start: 0.7644 (t-100) cc_final: 0.7330 (t-100) REVERT: A 235 TYR cc_start: 0.8289 (m-80) cc_final: 0.7906 (m-80) REVERT: A 257 GLU cc_start: 0.7860 (mp0) cc_final: 0.7335 (mp0) REVERT: A 433 ARG cc_start: 0.5282 (ptt-90) cc_final: 0.4515 (ptp90) REVERT: B 147 TRP cc_start: 0.8456 (t-100) cc_final: 0.8180 (t-100) REVERT: B 218 ARG cc_start: 0.7406 (ptt180) cc_final: 0.7098 (ptt-90) REVERT: B 268 ARG cc_start: 0.7641 (tpt170) cc_final: 0.7306 (ttt90) REVERT: C 56 GLU cc_start: 0.7517 (pm20) cc_final: 0.7297 (pm20) REVERT: C 143 PHE cc_start: 0.6961 (p90) cc_final: 0.6083 (p90) REVERT: D 146 ASN cc_start: 0.8835 (t0) cc_final: 0.8461 (t0) REVERT: D 212 ASP cc_start: 0.8200 (m-30) cc_final: 0.7887 (m-30) REVERT: D 304 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.8342 (m-80) REVERT: E 318 LYS cc_start: 0.8896 (ptmt) cc_final: 0.8287 (pttp) REVERT: F 77 LYS cc_start: 0.8403 (mtmt) cc_final: 0.8154 (mtpt) REVERT: F 102 ASN cc_start: 0.9251 (m-40) cc_final: 0.8945 (m110) REVERT: F 188 GLU cc_start: 0.8521 (pm20) cc_final: 0.8245 (mp0) REVERT: G 206 LYS cc_start: 0.8375 (mmmt) cc_final: 0.7891 (mtmt) REVERT: H 34 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8778 (mm-30) REVERT: H 72 ILE cc_start: 0.8986 (tp) cc_final: 0.8764 (tp) REVERT: H 94 ASN cc_start: 0.8432 (p0) cc_final: 0.7399 (t0) REVERT: H 310 GLN cc_start: 0.8659 (tt0) cc_final: 0.8401 (mt0) REVERT: I 34 GLU cc_start: 0.8852 (tt0) cc_final: 0.8435 (tt0) REVERT: I 307 VAL cc_start: 0.9215 (OUTLIER) cc_final: 0.8991 (t) REVERT: J 90 ASN cc_start: 0.8465 (t0) cc_final: 0.8018 (t0) REVERT: J 99 HIS cc_start: 0.8321 (OUTLIER) cc_final: 0.7867 (p-80) REVERT: K 82 LYS cc_start: 0.8982 (ttmt) cc_final: 0.8583 (tttm) REVERT: K 90 ASN cc_start: 0.8796 (t0) cc_final: 0.8419 (t0) REVERT: K 99 HIS cc_start: 0.8442 (OUTLIER) cc_final: 0.6144 (p-80) outliers start: 72 outliers final: 43 residues processed: 292 average time/residue: 0.1937 time to fit residues: 85.4308 Evaluate side-chains 282 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 233 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 178 LEU 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 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 42 VAL 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 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 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 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 307 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 33 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 290 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 173 optimal weight: 0.9980 chunk 151 optimal weight: 0.6980 chunk 138 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 12 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 HIS ** B 156 ASN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.137363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.094318 restraints weight = 43051.833| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.84 r_work: 0.2750 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24807 Z= 0.152 Angle : 0.549 8.107 33959 Z= 0.285 Chirality : 0.040 0.171 3815 Planarity : 0.004 0.049 4261 Dihedral : 11.706 179.813 3983 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.39 % Allowed : 16.69 % Favored : 80.92 % 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: -0.92 (0.15), residues: 2949 helix: 1.24 (0.17), residues: 924 sheet: -0.18 (0.23), residues: 505 loop : -2.05 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 153 TYR 0.013 0.001 TYR I 304 PHE 0.013 0.001 PHE D 245 TRP 0.014 0.001 TRP I 49 HIS 0.010 0.001 HIS C 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (24807) covalent geometry : angle 0.54917 / 0.28 (33959) hydrogen bonds : bond 0.03062 / 2.10 ( 995) hydrogen bonds : angle 4.55127 / 3.20 ( 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: 55 poor density : 250 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 10 TRP cc_start: 0.5564 (OUTLIER) cc_final: 0.4549 (p-90) REVERT: A 28 LYS cc_start: 0.8047 (mtpp) cc_final: 0.7734 (pttt) REVERT: A 62 GLN cc_start: 0.7746 (mp10) cc_final: 0.7401 (mp10) REVERT: A 200 HIS cc_start: 0.8369 (t-90) cc_final: 0.7774 (t-90) REVERT: A 228 TRP cc_start: 0.7678 (t-100) cc_final: 0.7380 (t-100) REVERT: A 235 TYR cc_start: 0.8161 (m-80) cc_final: 0.7858 (m-80) REVERT: A 257 GLU cc_start: 0.7774 (mp0) cc_final: 0.7262 (mp0) REVERT: A 433 ARG cc_start: 0.5216 (ptt-90) cc_final: 0.4462 (ptp90) REVERT: B 189 ARG cc_start: 0.8236 (mtp85) cc_final: 0.7917 (mtp85) REVERT: B 268 ARG cc_start: 0.7595 (tpt170) cc_final: 0.7304 (ttt90) REVERT: C 143 PHE cc_start: 0.6893 (p90) cc_final: 0.6021 (p90) REVERT: D 146 ASN cc_start: 0.8711 (t0) cc_final: 0.8338 (t0) REVERT: D 212 ASP cc_start: 0.7971 (m-30) cc_final: 0.7582 (m-30) REVERT: D 304 TYR cc_start: 0.8750 (OUTLIER) cc_final: 0.8238 (m-80) REVERT: F 77 LYS cc_start: 0.8346 (mtmt) cc_final: 0.8032 (mtpt) REVERT: F 102 ASN cc_start: 0.9138 (m-40) cc_final: 0.8857 (m110) REVERT: F 188 GLU cc_start: 0.8291 (pm20) cc_final: 0.8059 (mp0) REVERT: F 258 LYS cc_start: 0.7199 (mmpt) cc_final: 0.6868 (mmpt) REVERT: G 185 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8048 (mmt-90) REVERT: G 206 LYS cc_start: 0.8349 (mmmt) cc_final: 0.7961 (mtmt) REVERT: H 34 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8674 (mm-30) REVERT: H 94 ASN cc_start: 0.8337 (p0) cc_final: 0.7313 (t0) REVERT: H 310 GLN cc_start: 0.8528 (tt0) cc_final: 0.8323 (mt0) REVERT: I 34 GLU cc_start: 0.8617 (tt0) cc_final: 0.8182 (tt0) REVERT: I 147 ASP cc_start: 0.8129 (t70) cc_final: 0.7915 (m-30) REVERT: J 90 ASN cc_start: 0.8394 (t0) cc_final: 0.8019 (t0) REVERT: J 99 HIS cc_start: 0.8314 (OUTLIER) cc_final: 0.7766 (p-80) REVERT: K 82 LYS cc_start: 0.8988 (ttmt) cc_final: 0.8413 (tttm) REVERT: K 90 ASN cc_start: 0.8773 (t0) cc_final: 0.8432 (t0) REVERT: K 99 HIS cc_start: 0.8330 (OUTLIER) cc_final: 0.5998 (p-80) outliers start: 55 outliers final: 38 residues processed: 286 average time/residue: 0.2020 time to fit residues: 87.2478 Evaluate side-chains 277 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 234 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 A residue 414 TRP 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 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 143 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 227 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 260 optimal weight: 2.9990 chunk 228 optimal weight: 0.1980 chunk 36 optimal weight: 9.9990 chunk 230 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 206 optimal weight: 2.9990 chunk 68 optimal weight: 0.1980 chunk 283 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 HIS ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN G 51 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.139151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.095926 restraints weight = 35511.191| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.26 r_work: 0.2749 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2590 r_free = 0.2590 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 = 0.2590 r_free = 0.2590 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24807 Z= 0.121 Angle : 0.525 8.360 33959 Z= 0.272 Chirality : 0.039 0.168 3815 Planarity : 0.004 0.055 4261 Dihedral : 11.584 179.719 3983 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.43 % Allowed : 17.04 % Favored : 80.53 % 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: -0.70 (0.15), residues: 2949 helix: 1.48 (0.17), residues: 922 sheet: -0.01 (0.23), residues: 490 loop : -1.95 (0.15), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 185 TYR 0.012 0.001 TYR F 290 PHE 0.012 0.001 PHE D 245 TRP 0.012 0.001 TRP I 49 HIS 0.009 0.001 HIS C 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (24807) covalent geometry : angle 0.52528 / 0.27 (33959) hydrogen bonds : bond 0.02882 / 1.98 ( 995) hydrogen bonds : angle 4.40993 / 3.10 ( 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 314 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 258 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 10 TRP cc_start: 0.5591 (OUTLIER) cc_final: 0.4689 (p-90) REVERT: A 28 LYS cc_start: 0.8013 (mtpp) cc_final: 0.7709 (pttt) REVERT: A 62 GLN cc_start: 0.7627 (mp10) cc_final: 0.7308 (mp10) REVERT: A 200 HIS cc_start: 0.8345 (t-90) cc_final: 0.7729 (t-90) REVERT: A 228 TRP cc_start: 0.7656 (t-100) cc_final: 0.7221 (t-100) REVERT: A 235 TYR cc_start: 0.8127 (m-80) cc_final: 0.7821 (m-80) REVERT: A 257 GLU cc_start: 0.7802 (mp0) cc_final: 0.7212 (mp0) REVERT: A 433 ARG cc_start: 0.5293 (ptt-90) cc_final: 0.4525 (ptp90) REVERT: B 170 ARG cc_start: 0.8439 (tmm-80) cc_final: 0.7561 (mtm110) REVERT: B 189 ARG cc_start: 0.8207 (mtp85) cc_final: 0.7877 (mtp85) REVERT: B 268 ARG cc_start: 0.7583 (tpt170) cc_final: 0.7338 (mtm180) REVERT: C 56 GLU cc_start: 0.7899 (pm20) cc_final: 0.7216 (pm20) REVERT: C 143 PHE cc_start: 0.6821 (p90) cc_final: 0.5966 (p90) REVERT: D 146 ASN cc_start: 0.8782 (t0) cc_final: 0.8401 (t0) REVERT: D 212 ASP cc_start: 0.8108 (m-30) cc_final: 0.7707 (m-30) REVERT: D 304 TYR cc_start: 0.8637 (OUTLIER) cc_final: 0.8273 (m-80) REVERT: F 77 LYS cc_start: 0.8474 (mtmt) cc_final: 0.7967 (mtpt) REVERT: F 188 GLU cc_start: 0.8320 (pm20) cc_final: 0.8022 (mp0) REVERT: G 105 SER cc_start: 0.9296 (m) cc_final: 0.8965 (p) REVERT: G 185 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8010 (mmt-90) REVERT: G 206 LYS cc_start: 0.8481 (mmmt) cc_final: 0.8035 (mtmt) REVERT: H 94 ASN cc_start: 0.8366 (p0) cc_final: 0.8102 (p0) REVERT: H 99 ASP cc_start: 0.9005 (m-30) cc_final: 0.8784 (m-30) REVERT: H 310 GLN cc_start: 0.8579 (tt0) cc_final: 0.8280 (mt0) REVERT: I 261 LYS cc_start: 0.8203 (mttt) cc_final: 0.7969 (mttt) REVERT: I 310 GLN cc_start: 0.8398 (mm110) cc_final: 0.8179 (mm110) REVERT: J 90 ASN cc_start: 0.8237 (t0) cc_final: 0.7830 (t0) REVERT: J 99 HIS cc_start: 0.8248 (OUTLIER) cc_final: 0.7540 (p-80) REVERT: K 82 LYS cc_start: 0.8959 (ttmt) cc_final: 0.8359 (tttm) REVERT: K 90 ASN cc_start: 0.8802 (t0) cc_final: 0.8480 (t0) REVERT: K 99 HIS cc_start: 0.8314 (OUTLIER) cc_final: 0.6049 (p-80) outliers start: 56 outliers final: 39 residues processed: 292 average time/residue: 0.2011 time to fit residues: 88.1442 Evaluate side-chains 289 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 245 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 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 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 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 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 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 333 ARG 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: 5.9990 chunk 59 optimal weight: 4.9990 chunk 235 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 164 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 225 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 HIS ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN E 148 GLN E 342 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 = 0.3651 r_free = 0.3651 target = 0.138553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.095491 restraints weight = 35874.178| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.24 r_work: 0.2809 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 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 = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2572 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24807 Z= 0.141 Angle : 0.537 8.591 33959 Z= 0.277 Chirality : 0.040 0.307 3815 Planarity : 0.004 0.049 4261 Dihedral : 11.557 179.967 3983 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.26 % Allowed : 17.38 % Favored : 80.36 % 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: -0.65 (0.15), residues: 2949 helix: 1.52 (0.17), residues: 926 sheet: 0.03 (0.23), residues: 490 loop : -1.92 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 185 TYR 0.012 0.001 TYR F 290 PHE 0.010 0.001 PHE D 245 TRP 0.011 0.001 TRP I 49 HIS 0.009 0.001 HIS C 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (24807) covalent geometry : angle 0.53717 / 0.28 (33959) hydrogen bonds : bond 0.02924 / 2.01 ( 995) hydrogen bonds : angle 4.40105 / 3.09 ( 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 303 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 251 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 TRP cc_start: 0.5708 (OUTLIER) cc_final: 0.4938 (p-90) REVERT: A 28 LYS cc_start: 0.7969 (mtpp) cc_final: 0.7660 (pttt) REVERT: A 62 GLN cc_start: 0.7616 (mp10) cc_final: 0.7288 (mp10) REVERT: A 200 HIS cc_start: 0.8413 (t-90) cc_final: 0.7796 (t-90) REVERT: A 228 TRP cc_start: 0.7572 (t-100) cc_final: 0.7141 (t-100) REVERT: A 235 TYR cc_start: 0.8157 (m-80) cc_final: 0.7862 (m-80) REVERT: A 257 GLU cc_start: 0.7793 (mp0) cc_final: 0.7208 (mp0) REVERT: A 433 ARG cc_start: 0.5319 (ptt-90) cc_final: 0.4550 (ptp90) REVERT: B 170 ARG cc_start: 0.8400 (tmm-80) cc_final: 0.7484 (mtm110) REVERT: B 189 ARG cc_start: 0.8300 (mtp85) cc_final: 0.7992 (mtp85) REVERT: C 56 GLU cc_start: 0.7914 (pm20) cc_final: 0.7177 (pm20) REVERT: C 143 PHE cc_start: 0.6916 (p90) cc_final: 0.6020 (p90) REVERT: C 186 TRP cc_start: 0.7456 (t-100) cc_final: 0.6941 (t-100) REVERT: D 146 ASN cc_start: 0.8796 (t0) cc_final: 0.8426 (t0) REVERT: D 212 ASP cc_start: 0.8134 (m-30) cc_final: 0.7736 (m-30) REVERT: D 304 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.8209 (m-80) REVERT: E 130 ASP cc_start: 0.8417 (m-30) cc_final: 0.8032 (t0) REVERT: E 318 LYS cc_start: 0.8894 (ptmt) cc_final: 0.8255 (pttp) REVERT: F 77 LYS cc_start: 0.8415 (mtmt) cc_final: 0.8187 (mtpt) REVERT: F 188 GLU cc_start: 0.8350 (pm20) cc_final: 0.8090 (mp0) REVERT: G 105 SER cc_start: 0.9288 (m) cc_final: 0.9015 (p) REVERT: G 185 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8112 (mmt-90) REVERT: G 206 LYS cc_start: 0.8496 (mmmt) cc_final: 0.8081 (mtmt) REVERT: H 69 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8400 (ttt180) REVERT: H 94 ASN cc_start: 0.8429 (p0) cc_final: 0.8188 (p0) REVERT: H 99 ASP cc_start: 0.8999 (m-30) cc_final: 0.8793 (m-30) REVERT: H 310 GLN cc_start: 0.8590 (tt0) cc_final: 0.8353 (mt0) REVERT: I 261 LYS cc_start: 0.8315 (mttt) cc_final: 0.8092 (mttt) REVERT: I 302 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8348 (mt-10) REVERT: J 90 ASN cc_start: 0.8392 (t0) cc_final: 0.8000 (t0) REVERT: J 99 HIS cc_start: 0.8322 (OUTLIER) cc_final: 0.7678 (p-80) REVERT: K 82 LYS cc_start: 0.9065 (ttmt) cc_final: 0.8527 (ttmt) REVERT: K 90 ASN cc_start: 0.8825 (t0) cc_final: 0.8531 (t0) REVERT: K 99 HIS cc_start: 0.8340 (OUTLIER) cc_final: 0.6136 (p-80) outliers start: 52 outliers final: 39 residues processed: 282 average time/residue: 0.2098 time to fit residues: 88.2349 Evaluate side-chains 284 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 238 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 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 414 TRP 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 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 69 ARG 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 302 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 118 optimal weight: 0.9980 chunk 291 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 235 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 191 optimal weight: 0.5980 chunk 199 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.139021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.096611 restraints weight = 33745.467| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.13 r_work: 0.2801 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 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 = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2593 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= 0.121 Angle : 0.525 9.064 33959 Z= 0.271 Chirality : 0.039 0.219 3815 Planarity : 0.004 0.050 4261 Dihedral : 11.478 179.406 3983 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.04 % Allowed : 17.82 % Favored : 80.14 % 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: -0.53 (0.15), residues: 2949 helix: 1.67 (0.17), residues: 923 sheet: 0.10 (0.23), residues: 473 loop : -1.86 (0.15), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 185 TYR 0.011 0.001 TYR F 290 PHE 0.017 0.001 PHE C 44 TRP 0.010 0.001 TRP I 49 HIS 0.009 0.001 HIS C 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (24807) covalent geometry : angle 0.52484 / 0.27 (33959) hydrogen bonds : bond 0.02826 / 1.95 ( 995) hydrogen bonds : angle 4.31312 / 3.04 ( 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 306 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 259 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: A 10 TRP cc_start: 0.5561 (OUTLIER) cc_final: 0.4815 (p-90) REVERT: A 28 LYS cc_start: 0.7947 (mtpp) cc_final: 0.7694 (pttt) REVERT: A 62 GLN cc_start: 0.7623 (mp10) cc_final: 0.7289 (mp10) REVERT: A 200 HIS cc_start: 0.8333 (t-90) cc_final: 0.7785 (t-90) REVERT: A 228 TRP cc_start: 0.7580 (t-100) cc_final: 0.7115 (t-100) REVERT: A 235 TYR cc_start: 0.8147 (m-80) cc_final: 0.7883 (m-80) REVERT: A 257 GLU cc_start: 0.7784 (mp0) cc_final: 0.7183 (mp0) REVERT: A 433 ARG cc_start: 0.5290 (ptt-90) cc_final: 0.4507 (ptp90) REVERT: B 147 TRP cc_start: 0.8412 (t-100) cc_final: 0.8183 (t-100) REVERT: B 170 ARG cc_start: 0.8376 (tmm-80) cc_final: 0.7472 (mtm110) REVERT: B 189 ARG cc_start: 0.8215 (mtp85) cc_final: 0.7911 (mtp85) REVERT: B 221 PHE cc_start: 0.8115 (m-80) cc_final: 0.7616 (m-80) REVERT: C 143 PHE cc_start: 0.6839 (p90) cc_final: 0.5983 (p90) REVERT: C 186 TRP cc_start: 0.7412 (t-100) cc_final: 0.6897 (t-100) REVERT: D 146 ASN cc_start: 0.8781 (t0) cc_final: 0.8414 (t0) REVERT: D 212 ASP cc_start: 0.8054 (m-30) cc_final: 0.7629 (m-30) REVERT: D 304 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.8185 (m-80) REVERT: E 130 ASP cc_start: 0.8410 (m-30) cc_final: 0.8070 (t0) REVERT: F 188 GLU cc_start: 0.8326 (pm20) cc_final: 0.8070 (mp0) REVERT: F 206 LYS cc_start: 0.8770 (mtmm) cc_final: 0.8489 (mmtt) REVERT: G 105 SER cc_start: 0.9260 (m) cc_final: 0.8954 (p) REVERT: G 185 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.8051 (mmt-90) REVERT: G 206 LYS cc_start: 0.8447 (mmmt) cc_final: 0.8029 (mtmt) REVERT: H 94 ASN cc_start: 0.8373 (p0) cc_final: 0.7217 (t0) REVERT: H 99 ASP cc_start: 0.8990 (m-30) cc_final: 0.8771 (m-30) REVERT: H 310 GLN cc_start: 0.8535 (tt0) cc_final: 0.8262 (mt0) REVERT: I 261 LYS cc_start: 0.8288 (mttt) cc_final: 0.8023 (mttt) REVERT: I 302 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8371 (mt-10) REVERT: J 90 ASN cc_start: 0.8453 (t0) cc_final: 0.8105 (t0) REVERT: J 99 HIS cc_start: 0.8229 (OUTLIER) cc_final: 0.7547 (p-80) REVERT: K 82 LYS cc_start: 0.9024 (ttmt) cc_final: 0.8457 (ttmt) REVERT: K 90 ASN cc_start: 0.8756 (t0) cc_final: 0.8462 (t0) REVERT: K 99 HIS cc_start: 0.8263 (OUTLIER) cc_final: 0.6075 (p-80) outliers start: 47 outliers final: 35 residues processed: 287 average time/residue: 0.1961 time to fit residues: 84.7135 Evaluate side-chains 286 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 245 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 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 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 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 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 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 I residue 302 GLU Chi-restraints excluded: chain J residue 99 HIS 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: 5.9990 chunk 240 optimal weight: 0.7980 chunk 249 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 chunk 270 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 230 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** 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 319 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.138958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.096515 restraints weight = 43678.173| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.70 r_work: 0.2731 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24807 Z= 0.126 Angle : 0.533 9.477 33959 Z= 0.273 Chirality : 0.039 0.188 3815 Planarity : 0.004 0.071 4261 Dihedral : 11.439 179.487 3983 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.96 % Allowed : 18.12 % Favored : 79.92 % 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: -0.48 (0.15), residues: 2949 helix: 1.74 (0.17), residues: 917 sheet: 0.07 (0.23), residues: 477 loop : -1.83 (0.15), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 185 TYR 0.010 0.001 TYR D 304 PHE 0.011 0.001 PHE C 44 TRP 0.015 0.001 TRP A 394 HIS 0.009 0.001 HIS C 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (24807) covalent geometry : angle 0.53268 / 0.27 (33959) hydrogen bonds : bond 0.02829 / 1.95 ( 995) hydrogen bonds : angle 4.29839 / 3.02 ( 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 295 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 250 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 10 TRP cc_start: 0.5511 (OUTLIER) cc_final: 0.4765 (p-90) REVERT: A 28 LYS cc_start: 0.7983 (mtpp) cc_final: 0.7736 (pttt) REVERT: A 62 GLN cc_start: 0.7642 (mp10) cc_final: 0.7293 (mp10) REVERT: A 200 HIS cc_start: 0.8264 (t-90) cc_final: 0.7656 (t-90) REVERT: A 228 TRP cc_start: 0.7583 (t-100) cc_final: 0.7125 (t-100) REVERT: A 235 TYR cc_start: 0.8078 (m-80) cc_final: 0.7828 (m-80) REVERT: A 257 GLU cc_start: 0.7748 (mp0) cc_final: 0.7148 (mp0) REVERT: A 433 ARG cc_start: 0.5275 (ptt-90) cc_final: 0.4504 (ptp90) REVERT: B 170 ARG cc_start: 0.8354 (tmm-80) cc_final: 0.7478 (mtm110) REVERT: B 189 ARG cc_start: 0.8155 (mtp85) cc_final: 0.7857 (mtp85) REVERT: B 221 PHE cc_start: 0.8156 (m-80) cc_final: 0.7670 (m-80) REVERT: C 44 PHE cc_start: 0.8193 (m-80) cc_final: 0.7778 (m-10) REVERT: C 56 GLU cc_start: 0.7864 (pm20) cc_final: 0.7265 (pm20) REVERT: C 143 PHE cc_start: 0.6781 (p90) cc_final: 0.5846 (p90) REVERT: C 186 TRP cc_start: 0.7351 (t-100) cc_final: 0.6815 (t-100) REVERT: D 146 ASN cc_start: 0.8729 (t0) cc_final: 0.8364 (t0) REVERT: D 212 ASP cc_start: 0.7925 (m-30) cc_final: 0.7495 (m-30) REVERT: D 304 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.8109 (m-80) REVERT: E 130 ASP cc_start: 0.8299 (m-30) cc_final: 0.7969 (t0) REVERT: F 188 GLU cc_start: 0.8221 (pm20) cc_final: 0.7996 (mp0) REVERT: F 206 LYS cc_start: 0.8805 (mtmm) cc_final: 0.8536 (mmtt) REVERT: G 105 SER cc_start: 0.9196 (m) cc_final: 0.8914 (p) REVERT: G 185 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8020 (mmt-90) REVERT: G 206 LYS cc_start: 0.8413 (mmmt) cc_final: 0.8017 (mtmt) REVERT: H 94 ASN cc_start: 0.8312 (p0) cc_final: 0.8052 (p0) REVERT: H 99 ASP cc_start: 0.8825 (m-30) cc_final: 0.8606 (m-30) REVERT: H 310 GLN cc_start: 0.8443 (tt0) cc_final: 0.8151 (mt0) REVERT: I 34 GLU cc_start: 0.8594 (tt0) cc_final: 0.8175 (tt0) REVERT: I 261 LYS cc_start: 0.8170 (mttt) cc_final: 0.7963 (mttt) REVERT: I 302 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8264 (mt-10) REVERT: I 310 GLN cc_start: 0.8200 (mm110) cc_final: 0.7957 (mm110) REVERT: J 90 ASN cc_start: 0.8435 (t0) cc_final: 0.8077 (t0) REVERT: J 99 HIS cc_start: 0.8162 (OUTLIER) cc_final: 0.7552 (p-80) REVERT: K 82 LYS cc_start: 0.8980 (ttmt) cc_final: 0.8388 (ttmt) REVERT: K 90 ASN cc_start: 0.8692 (t0) cc_final: 0.8387 (t0) REVERT: K 99 HIS cc_start: 0.8235 (OUTLIER) cc_final: 0.6049 (p-80) outliers start: 45 outliers final: 37 residues processed: 278 average time/residue: 0.1840 time to fit residues: 77.0294 Evaluate side-chains 288 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 245 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 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 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 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 38 ASP Chi-restraints excluded: chain F residue 78 THR 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 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 I residue 203 ARG Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain J residue 99 HIS 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: 0.9980 chunk 79 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 218 optimal weight: 0.0670 chunk 182 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.7980 overall best weight: 1.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.137512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.094158 restraints weight = 35866.932| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.22 r_work: 0.2775 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2545 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2545 r_free = 0.2545 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2545 r_free = 0.2545 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24807 Z= 0.174 Angle : 0.564 9.064 33959 Z= 0.288 Chirality : 0.040 0.183 3815 Planarity : 0.004 0.066 4261 Dihedral : 11.494 179.808 3983 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.04 % Allowed : 18.21 % Favored : 79.75 % 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: -0.56 (0.15), residues: 2949 helix: 1.61 (0.17), residues: 925 sheet: 0.09 (0.23), residues: 476 loop : -1.86 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 64 TYR 0.013 0.002 TYR C 97 PHE 0.013 0.001 PHE C 44 TRP 0.019 0.001 TRP A 394 HIS 0.009 0.001 HIS C 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (24807) covalent geometry : angle 0.56415 / 0.29 (33959) hydrogen bonds : bond 0.03024 / 2.08 ( 995) hydrogen bonds : angle 4.39176 / 3.08 ( 2830) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7159.42 seconds wall clock time: 123 minutes 13.76 seconds (7393.76 seconds total)