Starting phenix.real_space_refine on Sun Sep 13 15:38:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jzz_22585/09_2026/7jzz_22585.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jzz_22585/09_2026/7jzz_22585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jzz_22585/09_2026/7jzz_22585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jzz_22585/09_2026/7jzz_22585.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jzz_22585/09_2026/7jzz_22585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jzz_22585/09_2026/7jzz_22585.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7jzz_22585/09_2026/7jzz_22585.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jzz_22585/09_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-2.2.1-6174/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, 'RNAv2': 60} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 28, 'rna3p': 32} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 5.42, per 1000 atoms: 0.22 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: 1.60 Conformation dependent library (CDL) restraints added in 1.2 seconds 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5534 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 54 sheets defined 33.3% alpha, 20.6% beta 6 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 2.76 Creating SS restraints... Processing helix chain 'A' and resid 9 through 31 Processing helix chain 'A' and resid 38 through 47 removed outlier: 4.072A pdb=" N THR A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 60 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 114 through 122 removed outlier: 4.312A pdb=" N PHE A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 removed outlier: 3.766A pdb=" N GLU A 136 " --> pdb=" O ASN A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 161 removed outlier: 3.756A pdb=" N ALA A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY A 161 " --> pdb=" O GLN A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 196 through 211 Processing helix chain 'A' and resid 212 through 225 removed outlier: 3.668A pdb=" N ALA A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.521A pdb=" N ILE A 251 " --> pdb=" O PRO A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 258 removed outlier: 4.070A pdb=" N GLU A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 removed outlier: 4.497A pdb=" N GLN A 273 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 294 through 306 removed outlier: 3.553A pdb=" N SER A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 344 removed outlier: 4.506A pdb=" N ALA A 317 " --> pdb=" O HIS A 313 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 Processing helix chain 'A' and resid 363 through 369 removed outlier: 3.748A pdb=" N ALA A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.821A pdb=" N GLY A 381 " --> pdb=" O ARG A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 removed outlier: 4.080A pdb=" N ARG A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 409 through 430 Processing helix chain 'B' and resid 33 through 49 removed outlier: 3.955A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 removed outlier: 3.903A pdb=" N ASP B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 165 through 180 Processing helix chain 'B' and resid 189 through 204 removed outlier: 3.901A pdb=" N LEU B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 218 Processing helix chain 'C' and resid 16 through 36 removed outlier: 3.503A pdb=" N LEU C 20 " --> pdb=" O PRO C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 72 removed outlier: 3.917A pdb=" N ALA C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.506A pdb=" N LEU C 76 " --> pdb=" O ARG C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 121 Processing helix chain 'C' and resid 123 through 131 Processing helix chain 'C' and resid 132 through 136 removed outlier: 4.012A pdb=" N VAL C 135 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA C 136 " --> pdb=" O ASP C 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 132 through 136' Processing helix chain 'D' and resid 51 through 55 Processing helix chain 'D' and resid 130 through 148 Processing helix chain 'D' and resid 151 through 163 Processing helix chain 'D' and resid 208 through 223 removed outlier: 3.788A pdb=" N ALA D 213 " --> pdb=" O ALA D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 322 through 332 removed outlier: 3.542A pdb=" N LEU D 326 " --> pdb=" O ASP D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 82 through 92 removed outlier: 3.732A pdb=" N SER E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 148 Processing helix chain 'E' and resid 151 through 163 Processing helix chain 'E' and resid 209 through 223 removed outlier: 3.506A pdb=" N ALA E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 284 Processing helix chain 'E' and resid 293 through 297 removed outlier: 3.627A pdb=" N LEU E 296 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY E 297 " --> pdb=" O ASP E 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 293 through 297' Processing helix chain 'E' and resid 322 through 332 Processing helix chain 'E' and resid 338 through 352 Processing helix chain 'F' and resid 51 through 55 Processing helix chain 'F' and resid 82 through 91 Processing helix chain 'F' and resid 130 through 148 Processing helix chain 'F' and resid 151 through 163 removed outlier: 3.506A pdb=" N ARG F 155 " --> pdb=" O ALA F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 223 Processing helix chain 'F' and resid 275 through 284 Processing helix chain 'F' and resid 293 through 297 removed outlier: 3.728A pdb=" N LEU F 296 " --> pdb=" O GLU F 293 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY F 297 " --> pdb=" O ASP F 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 293 through 297' Processing helix chain 'F' and resid 322 through 332 Processing helix chain 'F' and resid 338 through 352 Processing helix chain 'G' and resid 82 through 91 Processing helix chain 'G' and resid 130 through 148 Processing helix chain 'G' and resid 151 through 163 Processing helix chain 'G' and resid 209 through 223 removed outlier: 3.556A pdb=" N ALA G 213 " --> pdb=" O ALA G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 275 through 284 Processing helix chain 'G' and resid 322 through 332 Processing helix chain 'G' and resid 338 through 352 Processing helix chain 'H' and resid 51 through 55 Processing helix chain 'H' and resid 82 through 92 removed outlier: 3.606A pdb=" N SER H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 148 Processing helix chain 'H' and resid 150 through 163 removed outlier: 3.526A pdb=" N ALA H 154 " --> pdb=" O PHE H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 223 Processing helix chain 'H' and resid 275 through 284 Processing helix chain 'H' and resid 322 through 331 removed outlier: 3.566A pdb=" N LEU H 326 " --> pdb=" O ASP H 322 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 352 Processing helix chain 'I' and resid 51 through 55 Processing helix chain 'I' and resid 82 through 90 Processing helix chain 'I' and resid 130 through 148 Processing helix chain 'I' and resid 152 through 163 Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 275 through 284 Processing helix chain 'I' and resid 322 through 332 removed outlier: 3.638A pdb=" N LEU I 326 " --> pdb=" O ASP I 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 352 Processing helix chain 'J' and resid 109 through 121 Processing helix chain 'K' and resid 109 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 69 Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 192 removed outlier: 6.251A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 192 removed outlier: 6.251A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY B 254 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N GLY B 285 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLY B 287 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N TRP B 289 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LEU B 248 " --> pdb=" O TRP B 289 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 267 removed outlier: 5.861A pdb=" N LEU A 265 " --> pdb=" O TRP B 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 54 through 61 removed outlier: 4.012A pdb=" N VAL B 59 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU B 110 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 65 through 68 removed outlier: 5.093A pdb=" N ALA B 103 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN B 19 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER B 16 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA9, first strand: chain 'B' and resid 221 through 222 Processing sheet with id=AB1, first strand: chain 'B' and resid 304 through 306 removed outlier: 3.617A pdb=" N SER B 317 " --> pdb=" O TYR B 304 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 41 through 43 removed outlier: 3.501A pdb=" N HIS C 3 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 41 through 43 removed outlier: 3.501A pdb=" N HIS C 3 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AB5, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB6, first strand: chain 'C' and resid 172 through 173 removed outlier: 3.876A pdb=" N GLY C 172 " --> pdb=" O LYS C 180 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 127 through 128 Processing sheet with id=AB8, first strand: chain 'D' and resid 38 through 39 removed outlier: 4.058A pdb=" N VAL D 228 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG D 191 " --> pdb=" O HIS D 183 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 38 through 39 Processing sheet with id=AC1, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AC2, first strand: chain 'D' and resid 248 through 249 removed outlier: 4.300A pdb=" N THR D 264 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 285 through 287 Processing sheet with id=AC4, first strand: chain 'D' and resid 306 through 307 Processing sheet with id=AC5, first strand: chain 'E' and resid 127 through 128 Processing sheet with id=AC6, first strand: chain 'E' and resid 38 through 39 removed outlier: 4.103A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU E 229 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL E 177 " --> pdb=" O ASP E 196 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASP E 196 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL E 179 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARG E 194 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE E 181 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA E 192 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N HIS E 183 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 38 through 39 Processing sheet with id=AC8, first strand: chain 'E' and resid 63 through 70 Processing sheet with id=AC9, first strand: chain 'E' and resid 248 through 249 removed outlier: 4.417A pdb=" N THR E 264 " --> pdb=" O GLU E 249 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 285 through 287 Processing sheet with id=AD2, first strand: chain 'E' and resid 306 through 307 removed outlier: 3.741A pdb=" N LYS E 312 " --> pdb=" O VAL E 307 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 127 through 128 Processing sheet with id=AD4, first strand: chain 'F' and resid 38 through 39 removed outlier: 4.095A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU F 229 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL F 177 " --> pdb=" O ASP F 196 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ASP F 196 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL F 179 " --> pdb=" O ARG F 194 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG F 194 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE F 181 " --> pdb=" O ALA F 192 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ALA F 192 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N HIS F 183 " --> pdb=" O ALA F 190 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 38 through 39 Processing sheet with id=AD6, first strand: chain 'F' and resid 63 through 70 Processing sheet with id=AD7, first strand: chain 'F' and resid 285 through 287 Processing sheet with id=AD8, first strand: chain 'F' and resid 306 through 307 removed outlier: 3.658A pdb=" N LYS F 312 " --> pdb=" O VAL F 307 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 127 through 128 Processing sheet with id=AE1, first strand: chain 'G' and resid 38 through 39 removed outlier: 4.209A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL G 177 " --> pdb=" O ASP G 196 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ASP G 196 " --> pdb=" O VAL G 177 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL G 179 " --> pdb=" O ARG G 194 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG G 194 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE G 181 " --> pdb=" O ALA G 192 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA G 192 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N HIS G 183 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 38 through 39 Processing sheet with id=AE3, first strand: chain 'G' and resid 64 through 70 removed outlier: 4.284A pdb=" N PHE J 104 " --> pdb=" O LEU G 95 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N THR G 97 " --> pdb=" O PHE J 104 " (cutoff:3.500A) removed outlier: 11.660A pdb=" N CYS J 106 " --> pdb=" O THR G 97 " (cutoff:3.500A) removed outlier: 14.496A pdb=" N ASP G 99 " --> pdb=" O CYS J 106 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N PHE J 104 " --> pdb=" O LYS J 94 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LYS J 94 " --> pdb=" O PHE J 104 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 248 through 249 removed outlier: 4.600A pdb=" N THR G 264 " --> pdb=" O GLU G 249 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 285 through 287 Processing sheet with id=AE6, first strand: chain 'G' and resid 306 through 307 Processing sheet with id=AE7, first strand: chain 'H' and resid 127 through 128 Processing sheet with id=AE8, first strand: chain 'H' and resid 38 through 39 removed outlier: 4.055A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG H 191 " --> pdb=" O HIS H 183 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 38 through 39 Processing sheet with id=AF1, first strand: chain 'H' and resid 63 through 70 removed outlier: 3.579A pdb=" N ASN H 94 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA H 101 " --> pdb=" O VAL H 244 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 285 through 287 Processing sheet with id=AF3, first strand: chain 'H' and resid 306 through 307 removed outlier: 3.535A pdb=" N LYS H 312 " --> pdb=" O VAL H 307 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 127 through 128 Processing sheet with id=AF5, first strand: chain 'I' and resid 38 through 39 removed outlier: 4.697A pdb=" N LEU I 229 " --> pdb=" O ILE I 184 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 189 through 192 removed outlier: 6.666A pdb=" N HIS I 183 " --> pdb=" O ALA I 190 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA I 192 " --> pdb=" O ILE I 181 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE I 181 " --> pdb=" O ALA I 192 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU I 229 " --> pdb=" O ILE I 184 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 63 through 70 removed outlier: 3.583A pdb=" N VAL I 68 " --> pdb=" O GLN I 96 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA I 101 " --> pdb=" O VAL I 244 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 63 through 70 removed outlier: 3.583A pdb=" N VAL I 68 " --> pdb=" O GLN I 96 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N THR I 97 " --> pdb=" O PHE K 104 " (cutoff:3.500A) removed outlier: 11.844A pdb=" N CYS K 106 " --> pdb=" O THR I 97 " (cutoff:3.500A) removed outlier: 14.427A pdb=" N ASP I 99 " --> pdb=" O CYS K 106 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N PHE K 104 " --> pdb=" O LYS K 94 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LYS K 94 " --> pdb=" O PHE K 104 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 285 through 287 1022 hydrogen bonds defined for protein. 2802 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 4.60 Time building geometry restraints manager: 2.23 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 1.20e-02 6.94e+03 3.20e+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: 32181 2.08 - 4.16: 1491 4.16 - 6.23: 230 6.23 - 8.31: 45 8.31 - 10.39: 9 Bond angle restraints: 33956 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 33951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.69: 13376 21.69 - 43.39: 1076 43.39 - 65.08: 257 65.08 - 86.77: 48 86.77 - 108.47: 1 Dihedral angle restraints: 14758 sinusoidal: 6184 harmonic: 8574 Sorted by residual: dihedral pdb=" C4' C M 37 " pdb=" C3' C M 37 " pdb=" C2' C M 37 " pdb=" C1' C M 37 " ideal model delta sinusoidal sigma weight residual 36.34 -39.85 76.19 1 3.10e+00 1.04e-01 7.61e+02 dihedral pdb=" C4' G M 40 " pdb=" C3' G M 40 " pdb=" C2' G M 40 " pdb=" C1' G M 40 " ideal model delta sinusoidal sigma weight residual 36.34 -38.60 74.94 1 3.10e+00 1.04e-01 7.39e+02 dihedral pdb=" C4' G M 19 " pdb=" C3' G M 19 " pdb=" C2' G M 19 " pdb=" C1' G M 19 " ideal model delta sinusoidal sigma weight residual 36.35 -38.40 74.74 1 3.10e+00 1.04e-01 7.36e+02 ... (remaining 14755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2966 0.066 - 0.132: 662 0.132 - 0.198: 99 0.198 - 0.264: 62 0.264 - 0.330: 26 Chirality restraints: 3815 Sorted by residual: chirality pdb=" P A M 3 " pdb=" OP1 A M 3 " pdb=" OP2 A M 3 " pdb=" O5' A M 3 " both_signs ideal model delta sigma weight residual True 2.17 -2.50 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" C3' G M 40 " pdb=" C4' G M 40 " pdb=" O3' G M 40 " pdb=" C2' G M 40 " both_signs ideal model delta sigma weight residual False -2.50 -2.82 0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" C2' A M 45 " pdb=" C3' A M 45 " pdb=" O2' A M 45 " pdb=" C1' A M 45 " both_signs ideal model delta sigma weight residual False -2.79 -2.47 -0.32 2.00e-01 2.50e+01 2.57e+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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.910 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.750 ------------------------------------------------------------------------------- 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 : 0.011 0.088 24807 Z= 0.464 Angle : 1.019 10.390 33956 Z= 0.556 Chirality : 0.066 0.330 3815 Planarity : 0.007 0.080 4261 Dihedral : 16.985 108.465 9224 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 0.01051 / 0.46 (24807) covalent geometry : angle 1.01941 / 0.56 (33956) 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 : 0.844 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: 0.2184 time to fit residues: 107.4171 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 : 0.908 ------------------------------------------------------------------------------- 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 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN C 84 GLN C 108 ASN ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.139385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.096298 restraints weight = 33751.750| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.15 r_work: 0.2800 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24807 Z= 0.163 Angle : 0.898 18.207 33956 Z= 0.394 Chirality : 0.071 0.860 3815 Planarity : 0.005 0.059 4261 Dihedral : 12.406 159.507 3984 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.48 % Allowed : 12.17 % Favored : 86.35 % 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: -2.32 (0.13), residues: 2949 helix: -0.62 (0.15), residues: 925 sheet: -0.79 (0.22), residues: 499 loop : -2.46 (0.13), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 69 TYR 0.018 0.002 TYR C 97 PHE 0.022 0.001 PHE A 391 TRP 0.014 0.001 TRP G 49 HIS 0.006 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (24807) covalent geometry : angle 0.89845 / 0.39 (33956) hydrogen bonds : bond 0.03968 / 2.71 ( 995) hydrogen bonds : angle 5.25434 / 3.70 ( 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 314 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 280 time to evaluate : 0.914 Fit side-chains REVERT: A 10 TRP cc_start: 0.5909 (OUTLIER) cc_final: 0.4423 (p-90) REVERT: A 62 GLN cc_start: 0.7877 (mp10) cc_final: 0.7665 (mp10) REVERT: A 200 HIS cc_start: 0.8417 (t-90) cc_final: 0.7854 (t-90) REVERT: A 235 TYR cc_start: 0.8279 (m-80) cc_final: 0.7792 (m-80) REVERT: B 189 ARG cc_start: 0.8196 (mtp85) cc_final: 0.7869 (mtp85) REVERT: B 218 ARG cc_start: 0.7523 (ptt180) cc_final: 0.6990 (ptt-90) REVERT: B 268 ARG cc_start: 0.7603 (tpt170) cc_final: 0.7193 (ttt90) REVERT: C 44 PHE cc_start: 0.8538 (m-80) cc_final: 0.8244 (m-10) REVERT: C 84 GLN cc_start: 0.7762 (pt0) cc_final: 0.7490 (pt0) REVERT: C 143 PHE cc_start: 0.7238 (p90) cc_final: 0.6319 (p90) REVERT: D 294 ASP cc_start: 0.7984 (t0) cc_final: 0.7649 (t0) REVERT: F 51 GLN cc_start: 0.8223 (pt0) cc_final: 0.7986 (pt0) REVERT: F 80 ASP cc_start: 0.8035 (m-30) cc_final: 0.7761 (m-30) REVERT: F 188 GLU cc_start: 0.8476 (pm20) cc_final: 0.8165 (pm20) REVERT: F 269 ARG cc_start: 0.8276 (ptp-170) cc_final: 0.8031 (ptp-170) REVERT: G 188 GLU cc_start: 0.8066 (mp0) cc_final: 0.7805 (mm-30) REVERT: G 206 LYS cc_start: 0.8385 (mmmt) cc_final: 0.7813 (mtmt) REVERT: H 72 ILE cc_start: 0.9040 (tp) cc_final: 0.8763 (tp) REVERT: H 94 ASN cc_start: 0.8478 (p0) cc_final: 0.7567 (t0) REVERT: H 324 TYR cc_start: 0.9313 (m-80) cc_final: 0.9018 (m-80) REVERT: I 34 GLU cc_start: 0.8893 (tt0) cc_final: 0.8480 (tt0) REVERT: I 73 SER cc_start: 0.9062 (m) cc_final: 0.8504 (p) REVERT: I 185 ARG cc_start: 0.7824 (tpp80) cc_final: 0.7432 (tpp-160) REVERT: I 254 LYS cc_start: 0.7814 (mmtt) cc_final: 0.7298 (mppt) REVERT: I 261 LYS cc_start: 0.8011 (mttt) cc_final: 0.7778 (mttt) REVERT: J 99 HIS cc_start: 0.8155 (OUTLIER) cc_final: 0.7457 (p-80) REVERT: J 110 GLN cc_start: 0.8477 (tp40) cc_final: 0.8276 (tp40) REVERT: J 114 ASN cc_start: 0.8187 (m-40) cc_final: 0.7963 (m-40) REVERT: K 81 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8301 (mt-10) REVERT: K 82 LYS cc_start: 0.8736 (ttmt) cc_final: 0.8450 (tttm) REVERT: K 90 ASN cc_start: 0.8605 (t0) cc_final: 0.8136 (t0) REVERT: K 99 HIS cc_start: 0.8089 (OUTLIER) cc_final: 0.5903 (p-80) outliers start: 34 outliers final: 15 residues processed: 305 average time/residue: 0.2065 time to fit residues: 93.9384 Evaluate side-chains 263 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 245 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 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 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 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: 2.9990 chunk 87 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 252 optimal weight: 6.9990 chunk 256 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 58 optimal weight: 20.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 ASN ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 HIS ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN E 163 ASN F 159 HIS G 51 GLN G 129 ASN G 163 ASN ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 ASN I 159 HIS I 183 HIS I 348 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.134211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.091463 restraints weight = 36075.943| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.29 r_work: 0.2649 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2514 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2492 r_free = 0.2492 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2492 r_free = 0.2492 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 (10 function evaluations) r_final: 0.2492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 24807 Z= 0.317 Angle : 0.831 17.010 33956 Z= 0.387 Chirality : 0.063 0.702 3815 Planarity : 0.005 0.056 4261 Dihedral : 12.662 164.814 3982 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.65 % Allowed : 13.78 % Favored : 83.57 % 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: -1.82 (0.14), residues: 2949 helix: 0.13 (0.16), residues: 927 sheet: -0.59 (0.22), residues: 504 loop : -2.36 (0.14), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 117 TYR 0.017 0.002 TYR G 324 PHE 0.015 0.002 PHE D 245 TRP 0.024 0.002 TRP E 49 HIS 0.010 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00727 / 0.32 (24807) covalent geometry : angle 0.83068 / 0.39 (33956) hydrogen bonds : bond 0.03991 / 2.75 ( 995) hydrogen bonds : angle 5.07335 / 3.56 ( 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 301 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 240 time to evaluate : 0.884 Fit side-chains REVERT: A 10 TRP cc_start: 0.5924 (OUTLIER) cc_final: 0.4635 (p-90) REVERT: A 62 GLN cc_start: 0.7549 (mp10) cc_final: 0.7249 (mp10) REVERT: A 200 HIS cc_start: 0.8517 (t-90) cc_final: 0.7982 (t-90) REVERT: A 228 TRP cc_start: 0.7678 (t-100) cc_final: 0.7401 (t-100) REVERT: A 235 TYR cc_start: 0.8307 (m-80) cc_final: 0.7950 (m-80) REVERT: A 433 ARG cc_start: 0.5196 (ptt-90) cc_final: 0.4346 (ptp90) REVERT: B 147 TRP cc_start: 0.8480 (t-100) cc_final: 0.8226 (t-100) REVERT: B 268 ARG cc_start: 0.7637 (tpt170) cc_final: 0.7347 (ttt90) REVERT: B 306 HIS cc_start: 0.7988 (m-70) cc_final: 0.7720 (m-70) REVERT: C 1 MET cc_start: 0.6556 (mtt) cc_final: 0.5740 (ttp) REVERT: C 143 PHE cc_start: 0.6998 (p90) cc_final: 0.6099 (p90) REVERT: D 146 ASN cc_start: 0.8770 (t0) cc_final: 0.8379 (t0) REVERT: D 212 ASP cc_start: 0.8064 (m-30) cc_final: 0.7799 (m-30) REVERT: D 294 ASP cc_start: 0.8042 (t0) cc_final: 0.7705 (t0) REVERT: D 304 TYR cc_start: 0.8793 (OUTLIER) cc_final: 0.8404 (m-80) REVERT: F 269 ARG cc_start: 0.8497 (ptp-170) cc_final: 0.8257 (ptp-170) REVERT: G 186 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8250 (mp10) REVERT: G 188 GLU cc_start: 0.8531 (mp0) cc_final: 0.8081 (mm-30) REVERT: G 206 LYS cc_start: 0.8339 (mmmt) cc_final: 0.7766 (mtmt) REVERT: H 34 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8795 (mm-30) REVERT: H 72 ILE cc_start: 0.9047 (tp) cc_final: 0.8774 (tp) REVERT: H 94 ASN cc_start: 0.8433 (p0) cc_final: 0.7545 (t0) REVERT: I 34 GLU cc_start: 0.8925 (tt0) cc_final: 0.8478 (tt0) REVERT: I 185 ARG cc_start: 0.7951 (tpp80) cc_final: 0.7588 (tpp-160) REVERT: I 254 LYS cc_start: 0.7939 (mmtt) cc_final: 0.7403 (mppt) REVERT: I 261 LYS cc_start: 0.8283 (mttt) cc_final: 0.8072 (mttt) REVERT: J 99 HIS cc_start: 0.8263 (OUTLIER) cc_final: 0.7724 (p-80) REVERT: J 110 GLN cc_start: 0.8579 (tp40) cc_final: 0.8378 (tp40) REVERT: K 82 LYS cc_start: 0.8871 (ttmt) cc_final: 0.8303 (tttm) REVERT: K 90 ASN cc_start: 0.8852 (t0) cc_final: 0.8378 (t0) REVERT: K 99 HIS cc_start: 0.8456 (OUTLIER) cc_final: 0.5882 (p-80) outliers start: 61 outliers final: 40 residues processed: 277 average time/residue: 0.1910 time to fit residues: 79.8642 Evaluate side-chains 262 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 218 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 A residue 423 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 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 251 ILE 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 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 H residue 71 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 106 ASP 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 109 THR Chi-restraints excluded: chain I residue 143 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 Chi-restraints excluded: chain K residue 117 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 295 optimal weight: 3.9990 chunk 4 optimal weight: 20.0000 chunk 188 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 279 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 35 optimal weight: 0.0020 chunk 201 optimal weight: 3.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- 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 153 GLN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 GLN G 129 ASN ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 348 ASN ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.135937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.093249 restraints weight = 35697.186| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.21 r_work: 0.2704 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2548 r_free = 0.2548 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 = 0.2548 r_free = 0.2548 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 24807 Z= 0.214 Angle : 0.734 15.648 33956 Z= 0.341 Chirality : 0.055 0.633 3815 Planarity : 0.004 0.051 4261 Dihedral : 12.632 170.647 3982 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.00 % Allowed : 14.91 % Favored : 82.09 % 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: -1.41 (0.15), residues: 2949 helix: 0.67 (0.16), residues: 924 sheet: -0.39 (0.22), residues: 501 loop : -2.24 (0.14), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 237 TYR 0.015 0.002 TYR F 290 PHE 0.019 0.001 PHE D 245 TRP 0.016 0.001 TRP I 49 HIS 0.010 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 (24807) covalent geometry : angle 0.73427 / 0.34 (33956) hydrogen bonds : bond 0.03467 / 2.38 ( 995) hydrogen bonds : angle 4.80159 / 3.36 ( 2830) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 250 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 10 TRP cc_start: 0.5857 (OUTLIER) cc_final: 0.4641 (p-90) REVERT: A 62 GLN cc_start: 0.7569 (mp10) cc_final: 0.7236 (mp10) REVERT: A 178 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8495 (mt) REVERT: A 200 HIS cc_start: 0.8470 (t-90) cc_final: 0.7919 (t-90) REVERT: A 228 TRP cc_start: 0.7610 (t-100) cc_final: 0.7307 (t-100) REVERT: A 235 TYR cc_start: 0.8262 (m-80) cc_final: 0.7899 (m-80) REVERT: A 433 ARG cc_start: 0.5177 (ptt-90) cc_final: 0.4353 (ptp90) REVERT: B 147 TRP cc_start: 0.8511 (t-100) cc_final: 0.8275 (t-100) REVERT: B 268 ARG cc_start: 0.7648 (tpt170) cc_final: 0.7285 (ttt90) REVERT: B 306 HIS cc_start: 0.7939 (m-70) cc_final: 0.7723 (m-70) REVERT: C 143 PHE cc_start: 0.7088 (p90) cc_final: 0.6201 (p90) REVERT: D 146 ASN cc_start: 0.8776 (t0) cc_final: 0.8427 (t0) REVERT: D 212 ASP cc_start: 0.8139 (m-30) cc_final: 0.7880 (m-30) REVERT: D 249 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8306 (mm-30) REVERT: D 294 ASP cc_start: 0.7930 (t0) cc_final: 0.7634 (t0) REVERT: D 304 TYR cc_start: 0.8745 (OUTLIER) cc_final: 0.8339 (m-80) REVERT: E 316 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8248 (mm-40) REVERT: F 102 ASN cc_start: 0.9260 (m-40) cc_final: 0.8905 (m110) REVERT: G 188 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8078 (mm-30) REVERT: G 206 LYS cc_start: 0.8387 (mmmt) cc_final: 0.7894 (mtmt) REVERT: H 72 ILE cc_start: 0.9039 (tp) cc_final: 0.8760 (tp) REVERT: H 94 ASN cc_start: 0.8438 (p0) cc_final: 0.7583 (t0) REVERT: I 34 GLU cc_start: 0.8867 (tt0) cc_final: 0.8434 (tt0) REVERT: I 185 ARG cc_start: 0.7883 (tpp80) cc_final: 0.7527 (tpp-160) REVERT: I 254 LYS cc_start: 0.7967 (mmtt) cc_final: 0.7497 (mppt) REVERT: I 348 ASN cc_start: 0.9249 (OUTLIER) cc_final: 0.9031 (t0) REVERT: J 90 ASN cc_start: 0.8379 (t0) cc_final: 0.8021 (t0) REVERT: J 99 HIS cc_start: 0.8275 (OUTLIER) cc_final: 0.7719 (p-80) REVERT: K 82 LYS cc_start: 0.8961 (ttmt) cc_final: 0.8381 (tttm) REVERT: K 90 ASN cc_start: 0.8836 (t0) cc_final: 0.8423 (t0) REVERT: K 99 HIS cc_start: 0.8435 (OUTLIER) cc_final: 0.6160 (p-80) outliers start: 69 outliers final: 36 residues processed: 299 average time/residue: 0.1980 time to fit residues: 89.4969 Evaluate side-chains 270 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 226 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 153 ARG Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 196 THR 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 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 307 VAL Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain E residue 316 GLN 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 94 ASN Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 203 ARG 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 44 MET Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 348 ASN Chi-restraints excluded: chain J residue 99 HIS Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 117 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 32 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 166 optimal weight: 0.2980 chunk 30 optimal weight: 9.9990 chunk 283 optimal weight: 2.9990 chunk 197 optimal weight: 0.0470 chunk 146 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 141 optimal weight: 0.7980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 GLN A 203 HIS ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS C 153 GLN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 GLN G 51 GLN G 148 GLN ** 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 342 GLN ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.140566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.097580 restraints weight = 34026.574| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.17 r_work: 0.2854 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2385 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= 0.121 Angle : 0.660 13.436 33956 Z= 0.307 Chirality : 0.049 0.502 3815 Planarity : 0.004 0.057 4261 Dihedral : 12.353 171.972 3982 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.43 % Allowed : 16.04 % Favored : 81.53 % 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: -0.99 (0.15), residues: 2949 helix: 1.21 (0.17), residues: 922 sheet: -0.30 (0.22), residues: 507 loop : -2.06 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 237 TYR 0.018 0.001 TYR I 304 PHE 0.019 0.001 PHE D 245 TRP 0.011 0.001 TRP A 414 HIS 0.009 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (24807) covalent geometry : angle 0.66041 / 0.31 (33956) hydrogen bonds : bond 0.03045 / 2.08 ( 995) hydrogen bonds : angle 4.52400 / 3.19 ( 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 324 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 268 time to evaluate : 1.056 Fit side-chains revert: symmetry clash REVERT: A 10 TRP cc_start: 0.5809 (OUTLIER) cc_final: 0.4754 (p-90) REVERT: A 28 LYS cc_start: 0.8065 (mtpp) cc_final: 0.7756 (pttt) REVERT: A 62 GLN cc_start: 0.7789 (mp10) cc_final: 0.7460 (mp10) REVERT: A 178 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8760 (mt) REVERT: A 200 HIS cc_start: 0.8416 (t-90) cc_final: 0.7902 (t-90) REVERT: A 228 TRP cc_start: 0.7666 (t-100) cc_final: 0.7352 (t-100) REVERT: A 235 TYR cc_start: 0.8217 (m-80) cc_final: 0.7884 (m-80) REVERT: A 257 GLU cc_start: 0.7845 (mp0) cc_final: 0.7316 (mp0) REVERT: A 433 ARG cc_start: 0.5192 (ptt-90) cc_final: 0.4451 (ptp90) REVERT: B 268 ARG cc_start: 0.7661 (tpt170) cc_final: 0.7381 (ttt90) REVERT: C 56 GLU cc_start: 0.7904 (pm20) cc_final: 0.7206 (pm20) REVERT: C 84 GLN cc_start: 0.7635 (pt0) cc_final: 0.7405 (pt0) REVERT: C 143 PHE cc_start: 0.7080 (p90) cc_final: 0.6213 (p90) REVERT: D 146 ASN cc_start: 0.8683 (t0) cc_final: 0.8336 (t0) REVERT: D 212 ASP cc_start: 0.8138 (m-30) cc_final: 0.7786 (m-30) REVERT: D 249 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8177 (mm-30) REVERT: F 188 GLU cc_start: 0.8395 (pm20) cc_final: 0.8152 (mp0) REVERT: F 258 LYS cc_start: 0.7298 (mmpt) cc_final: 0.6985 (mmpt) REVERT: G 188 GLU cc_start: 0.8290 (mp0) cc_final: 0.8007 (mm-30) REVERT: G 206 LYS cc_start: 0.8458 (mmmt) cc_final: 0.8084 (mtmt) REVERT: H 72 ILE cc_start: 0.8963 (tp) cc_final: 0.8739 (tp) REVERT: H 94 ASN cc_start: 0.8534 (p0) cc_final: 0.7426 (t0) REVERT: H 310 GLN cc_start: 0.8711 (tt0) cc_final: 0.8415 (mt0) REVERT: I 34 GLU cc_start: 0.8816 (tt0) cc_final: 0.8439 (tt0) REVERT: I 99 ASP cc_start: 0.8857 (m-30) cc_final: 0.8435 (m-30) REVERT: I 147 ASP cc_start: 0.8355 (t70) cc_final: 0.7909 (m-30) REVERT: I 203 ARG cc_start: 0.8524 (ptp-110) cc_final: 0.7927 (mtp85) REVERT: I 261 LYS cc_start: 0.8298 (mttt) cc_final: 0.7737 (mttt) REVERT: I 348 ASN cc_start: 0.9228 (OUTLIER) cc_final: 0.8998 (t0) REVERT: J 90 ASN cc_start: 0.8469 (t0) cc_final: 0.8117 (t0) REVERT: J 99 HIS cc_start: 0.8348 (OUTLIER) cc_final: 0.7738 (p-80) REVERT: K 82 LYS cc_start: 0.9046 (ttmt) cc_final: 0.8519 (tttm) REVERT: K 90 ASN cc_start: 0.8890 (t0) cc_final: 0.8565 (t0) REVERT: K 99 HIS cc_start: 0.8334 (OUTLIER) cc_final: 0.6150 (p-80) outliers start: 56 outliers final: 38 residues processed: 299 average time/residue: 0.1876 time to fit residues: 85.4351 Evaluate side-chains 279 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 236 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 178 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 196 THR 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 C residue 100 VAL Chi-restraints excluded: chain C residue 151 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 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 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 F residue 308 THR 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 237 ARG Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 304 TYR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 304 TYR Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain I residue 348 ASN Chi-restraints excluded: chain J residue 99 HIS Chi-restraints excluded: chain K residue 99 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 33 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 chunk 63 optimal weight: 7.9990 chunk 290 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 173 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 12 optimal weight: 9.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 ASN ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS C 153 GLN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 GLN E 342 GLN F 94 ASN ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.136980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.094606 restraints weight = 43464.996| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.91 r_work: 0.2678 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2513 r_free = 0.2513 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2513 r_free = 0.2513 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 24807 Z= 0.222 Angle : 0.717 14.095 33956 Z= 0.334 Chirality : 0.054 0.578 3815 Planarity : 0.004 0.047 4261 Dihedral : 12.400 175.826 3982 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.43 % Allowed : 16.78 % Favored : 80.79 % 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: -0.97 (0.15), residues: 2949 helix: 1.22 (0.17), residues: 923 sheet: -0.32 (0.22), residues: 515 loop : -2.06 (0.15), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 111 TYR 0.016 0.002 TYR I 304 PHE 0.019 0.001 PHE D 245 TRP 0.016 0.001 TRP A 394 HIS 0.010 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.22 (24807) covalent geometry : angle 0.71706 / 0.33 (33956) hydrogen bonds : bond 0.03327 / 2.28 ( 995) hydrogen bonds : angle 4.61566 / 3.24 ( 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 295 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 239 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 10 TRP cc_start: 0.5803 (OUTLIER) cc_final: 0.4877 (p-90) REVERT: A 28 LYS cc_start: 0.8039 (mtpp) cc_final: 0.7716 (pttt) REVERT: A 62 GLN cc_start: 0.7655 (mp10) cc_final: 0.7296 (mp10) REVERT: A 178 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8656 (mt) REVERT: A 200 HIS cc_start: 0.8423 (t-90) cc_final: 0.7805 (t-90) REVERT: A 228 TRP cc_start: 0.7635 (t-100) cc_final: 0.7305 (t-100) REVERT: A 235 TYR cc_start: 0.8231 (m-80) cc_final: 0.7891 (m-80) REVERT: A 257 GLU cc_start: 0.7876 (mp0) cc_final: 0.7336 (mp0) REVERT: A 433 ARG cc_start: 0.5313 (ptt-90) cc_final: 0.4531 (ptp90) REVERT: B 147 TRP cc_start: 0.8319 (t-100) cc_final: 0.8017 (t-100) REVERT: B 218 ARG cc_start: 0.7246 (ptt180) cc_final: 0.6980 (ptt-90) REVERT: B 268 ARG cc_start: 0.7676 (tpt170) cc_final: 0.7358 (ttt90) REVERT: C 1 MET cc_start: 0.6411 (mtt) cc_final: 0.5820 (ptm) REVERT: C 56 GLU cc_start: 0.7868 (pm20) cc_final: 0.7154 (pm20) REVERT: C 143 PHE cc_start: 0.6953 (p90) cc_final: 0.6056 (p90) REVERT: D 146 ASN cc_start: 0.8814 (t0) cc_final: 0.8474 (t0) REVERT: D 212 ASP cc_start: 0.8130 (m-30) cc_final: 0.7741 (m-30) REVERT: D 249 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8216 (mm-30) REVERT: D 304 TYR cc_start: 0.8758 (OUTLIER) cc_final: 0.8332 (m-80) REVERT: F 258 LYS cc_start: 0.7155 (mmpt) cc_final: 0.6774 (mmpt) REVERT: G 65 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8826 (mt-10) REVERT: G 188 GLU cc_start: 0.8547 (mp0) cc_final: 0.8005 (mm-30) REVERT: G 206 LYS cc_start: 0.8419 (mmmt) cc_final: 0.7926 (mtmt) REVERT: H 72 ILE cc_start: 0.8987 (tp) cc_final: 0.8764 (tp) REVERT: H 94 ASN cc_start: 0.8536 (p0) cc_final: 0.7376 (t0) REVERT: H 310 GLN cc_start: 0.8663 (tt0) cc_final: 0.8368 (mt0) REVERT: I 34 GLU cc_start: 0.8904 (tt0) cc_final: 0.8504 (tt0) REVERT: I 147 ASP cc_start: 0.8397 (t70) cc_final: 0.7925 (m-30) REVERT: I 348 ASN cc_start: 0.9279 (OUTLIER) cc_final: 0.9051 (t0) REVERT: J 90 ASN cc_start: 0.8340 (t0) cc_final: 0.7992 (t0) REVERT: J 99 HIS cc_start: 0.8267 (OUTLIER) cc_final: 0.7814 (p-80) REVERT: K 82 LYS cc_start: 0.8982 (ttmt) cc_final: 0.8528 (ttmm) REVERT: K 90 ASN cc_start: 0.8853 (t0) cc_final: 0.8462 (t0) REVERT: K 99 HIS cc_start: 0.8499 (OUTLIER) cc_final: 0.6039 (p-80) outliers start: 56 outliers final: 45 residues processed: 273 average time/residue: 0.2022 time to fit residues: 83.2017 Evaluate side-chains 283 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 232 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 153 ARG 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 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 C residue 151 THR Chi-restraints excluded: chain C residue 153 GLN 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 250 LEU Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 203 ARG Chi-restraints excluded: chain G residue 237 ARG Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 304 TYR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 106 ASP 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 72 ILE Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain I residue 333 ARG Chi-restraints excluded: chain I residue 348 ASN Chi-restraints excluded: chain J residue 99 HIS 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: 20.0000 chunk 260 optimal weight: 0.7980 chunk 228 optimal weight: 2.9990 chunk 36 optimal weight: 0.0470 chunk 230 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 167 optimal weight: 0.7980 chunk 206 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 283 optimal weight: 2.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS C 153 GLN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.138866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.095614 restraints weight = 35589.522| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.18 r_work: 0.2799 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- 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: 0.8703 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24807 Z= 0.147 Angle : 0.672 13.654 33956 Z= 0.312 Chirality : 0.050 0.494 3815 Planarity : 0.004 0.047 4261 Dihedral : 12.297 176.432 3982 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.39 % Allowed : 17.08 % 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: -0.82 (0.15), residues: 2949 helix: 1.38 (0.17), residues: 924 sheet: -0.18 (0.23), residues: 495 loop : -1.99 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 185 TYR 0.016 0.001 TYR I 304 PHE 0.021 0.001 PHE D 245 TRP 0.012 0.001 TRP I 49 HIS 0.009 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (24807) covalent geometry : angle 0.67194 / 0.31 (33956) hydrogen bonds : bond 0.03096 / 2.13 ( 995) hydrogen bonds : angle 4.50384 / 3.17 ( 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 302 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 247 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 TRP cc_start: 0.5747 (OUTLIER) cc_final: 0.4784 (p-90) REVERT: A 28 LYS cc_start: 0.8012 (mtpp) cc_final: 0.7715 (pttt) REVERT: A 62 GLN cc_start: 0.7752 (mp10) cc_final: 0.7401 (mp10) REVERT: A 178 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8727 (mt) REVERT: A 200 HIS cc_start: 0.8425 (t-90) cc_final: 0.7846 (t-90) REVERT: A 228 TRP cc_start: 0.7540 (t-100) cc_final: 0.7154 (t-100) REVERT: A 235 TYR cc_start: 0.8185 (m-80) cc_final: 0.7899 (m-80) REVERT: A 257 GLU cc_start: 0.7813 (mp0) cc_final: 0.7300 (mp0) REVERT: A 433 ARG cc_start: 0.5293 (ptt-90) cc_final: 0.4526 (ptp90) REVERT: B 89 ASN cc_start: 0.8943 (m-40) cc_final: 0.8602 (m110) REVERT: B 147 TRP cc_start: 0.8459 (t-100) cc_final: 0.8234 (t-100) REVERT: B 268 ARG cc_start: 0.7680 (tpt170) cc_final: 0.7390 (ttt90) REVERT: C 1 MET cc_start: 0.6401 (mtt) cc_final: 0.5827 (ptm) REVERT: C 56 GLU cc_start: 0.7892 (pm20) cc_final: 0.7200 (pm20) REVERT: C 143 PHE cc_start: 0.6945 (p90) cc_final: 0.6023 (p90) REVERT: D 146 ASN cc_start: 0.8765 (t0) cc_final: 0.8433 (t0) REVERT: D 212 ASP cc_start: 0.8105 (m-30) cc_final: 0.7697 (m-30) REVERT: D 249 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8184 (mm-30) REVERT: D 304 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.8333 (m-80) REVERT: F 258 LYS cc_start: 0.7203 (mmpt) cc_final: 0.6977 (mmpt) REVERT: G 188 GLU cc_start: 0.8419 (mp0) cc_final: 0.7983 (mm-30) REVERT: G 206 LYS cc_start: 0.8431 (mmmt) cc_final: 0.8024 (mtmt) REVERT: H 94 ASN cc_start: 0.8493 (p0) cc_final: 0.7412 (t0) REVERT: H 99 ASP cc_start: 0.8982 (m-30) cc_final: 0.8755 (m-30) REVERT: H 310 GLN cc_start: 0.8631 (tt0) cc_final: 0.8373 (mt0) REVERT: I 34 GLU cc_start: 0.8855 (tt0) cc_final: 0.8451 (tt0) REVERT: I 147 ASP cc_start: 0.8184 (t70) cc_final: 0.7827 (m-30) REVERT: I 348 ASN cc_start: 0.9259 (OUTLIER) cc_final: 0.9027 (t0) REVERT: J 90 ASN cc_start: 0.8396 (t0) cc_final: 0.8050 (t0) REVERT: J 99 HIS cc_start: 0.8349 (OUTLIER) cc_final: 0.7833 (p-80) REVERT: K 82 LYS cc_start: 0.9046 (ttmt) cc_final: 0.8467 (tttm) REVERT: K 90 ASN cc_start: 0.8887 (t0) cc_final: 0.8540 (t0) REVERT: K 99 HIS cc_start: 0.8459 (OUTLIER) cc_final: 0.6066 (p-80) outliers start: 55 outliers final: 40 residues processed: 283 average time/residue: 0.1955 time to fit residues: 83.9263 Evaluate side-chains 282 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 236 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 153 ARG 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 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 38 ASP Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 237 ARG Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 304 TYR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 304 TYR Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain I residue 333 ARG Chi-restraints excluded: chain I residue 348 ASN Chi-restraints excluded: chain J residue 99 HIS 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: 0.5980 chunk 59 optimal weight: 3.9990 chunk 235 optimal weight: 0.7980 chunk 178 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 164 optimal weight: 0.5980 chunk 13 optimal weight: 20.0000 chunk 135 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 HIS C 153 GLN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 ASN I 148 GLN I 342 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.141094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.098232 restraints weight = 36411.796| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.25 r_work: 0.2865 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2722 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= 0.121 Angle : 0.639 13.011 33956 Z= 0.298 Chirality : 0.048 0.397 3815 Planarity : 0.004 0.045 4261 Dihedral : 12.087 178.273 3982 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.30 % Allowed : 17.43 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.15), residues: 2949 helix: 1.59 (0.17), residues: 922 sheet: -0.21 (0.22), residues: 511 loop : -1.90 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 69 TYR 0.015 0.001 TYR I 304 PHE 0.026 0.001 PHE D 245 TRP 0.010 0.001 TRP I 49 HIS 0.007 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (24807) covalent geometry : angle 0.63937 / 0.30 (33956) hydrogen bonds : bond 0.02884 / 1.98 ( 995) hydrogen bonds : angle 4.36625 / 3.07 ( 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 312 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 259 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 TRP cc_start: 0.5877 (OUTLIER) cc_final: 0.5065 (p-90) REVERT: A 28 LYS cc_start: 0.7943 (mtpp) cc_final: 0.7701 (pttt) REVERT: A 62 GLN cc_start: 0.7640 (mp10) cc_final: 0.7315 (mp10) REVERT: A 178 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8874 (mt) REVERT: A 200 HIS cc_start: 0.8373 (t-90) cc_final: 0.7800 (t-90) REVERT: A 228 TRP cc_start: 0.7600 (t-100) cc_final: 0.7184 (t-100) REVERT: A 235 TYR cc_start: 0.8126 (m-80) cc_final: 0.7832 (m-80) REVERT: A 257 GLU cc_start: 0.7824 (mp0) cc_final: 0.7293 (mp0) REVERT: A 433 ARG cc_start: 0.5309 (ptt-90) cc_final: 0.4552 (ptp90) REVERT: B 170 ARG cc_start: 0.8395 (tmm-80) cc_final: 0.7462 (mtm110) REVERT: C 56 GLU cc_start: 0.7919 (pm20) cc_final: 0.7195 (pm20) REVERT: C 143 PHE cc_start: 0.6910 (p90) cc_final: 0.6041 (p90) REVERT: C 186 TRP cc_start: 0.7439 (t-100) cc_final: 0.6910 (t-100) REVERT: D 146 ASN cc_start: 0.8774 (t0) cc_final: 0.8445 (t0) REVERT: D 212 ASP cc_start: 0.8096 (m-30) cc_final: 0.7689 (m-30) REVERT: D 304 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.8205 (m-80) REVERT: F 188 GLU cc_start: 0.8310 (pm20) cc_final: 0.8097 (mp0) REVERT: F 206 LYS cc_start: 0.8773 (mtmm) cc_final: 0.8498 (mmtt) REVERT: G 105 SER cc_start: 0.9238 (m) cc_final: 0.8949 (p) REVERT: G 185 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8059 (mmt-90) REVERT: G 188 GLU cc_start: 0.8291 (mp0) cc_final: 0.7989 (mm-30) REVERT: G 206 LYS cc_start: 0.8508 (mmmt) cc_final: 0.8115 (mtmt) REVERT: H 94 ASN cc_start: 0.8446 (p0) cc_final: 0.7091 (t0) REVERT: H 310 GLN cc_start: 0.8635 (tt0) cc_final: 0.8355 (mt0) REVERT: I 34 GLU cc_start: 0.8808 (tt0) cc_final: 0.8441 (tt0) REVERT: I 147 ASP cc_start: 0.8018 (t70) cc_final: 0.7749 (m-30) REVERT: I 348 ASN cc_start: 0.9273 (OUTLIER) cc_final: 0.9053 (t0) REVERT: J 90 ASN cc_start: 0.8388 (t0) cc_final: 0.7996 (t0) REVERT: J 99 HIS cc_start: 0.8321 (OUTLIER) cc_final: 0.7709 (p-80) REVERT: K 82 LYS cc_start: 0.9066 (ttmt) cc_final: 0.8548 (ttmt) REVERT: K 90 ASN cc_start: 0.8878 (t0) cc_final: 0.8579 (t0) REVERT: K 99 HIS cc_start: 0.8350 (OUTLIER) cc_final: 0.6159 (p-80) outliers start: 53 outliers final: 38 residues processed: 291 average time/residue: 0.2000 time to fit residues: 87.1239 Evaluate side-chains 288 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 243 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 153 ARG 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 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 C residue 151 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 251 ILE Chi-restraints excluded: chain F residue 304 TYR 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 H residue 78 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 304 TYR Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 247 SER Chi-restraints excluded: chain I residue 333 ARG Chi-restraints excluded: chain I residue 348 ASN 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: 0.8980 chunk 291 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 235 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 191 optimal weight: 0.5980 chunk 199 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS C 19 GLN C 153 GLN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 GLN E 148 GLN E 342 GLN F 94 ASN ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 94 ASN I 102 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.140085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.096933 restraints weight = 33922.321| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.19 r_work: 0.2801 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2765 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= 0.141 Angle : 0.649 12.939 33956 Z= 0.302 Chirality : 0.048 0.403 3815 Planarity : 0.004 0.043 4261 Dihedral : 12.072 179.851 3982 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.35 % Allowed : 17.69 % Favored : 79.97 % 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: -0.61 (0.15), residues: 2949 helix: 1.62 (0.17), residues: 925 sheet: -0.11 (0.23), residues: 490 loop : -1.89 (0.15), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 64 TYR 0.016 0.001 TYR I 304 PHE 0.023 0.001 PHE D 245 TRP 0.012 0.001 TRP A 394 HIS 0.009 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (24807) covalent geometry : angle 0.64916 / 0.30 (33956) hydrogen bonds : bond 0.02950 / 2.03 ( 995) hydrogen bonds : angle 4.36069 / 3.07 ( 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 300 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 246 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 TRP cc_start: 0.5824 (OUTLIER) cc_final: 0.5082 (p-90) REVERT: A 28 LYS cc_start: 0.7930 (mtpp) cc_final: 0.7682 (pttt) REVERT: A 62 GLN cc_start: 0.7612 (mp10) cc_final: 0.7284 (mp10) REVERT: A 178 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8766 (mt) REVERT: A 200 HIS cc_start: 0.8341 (t-90) cc_final: 0.7749 (t-90) REVERT: A 228 TRP cc_start: 0.7569 (t-100) cc_final: 0.7184 (t-100) REVERT: A 235 TYR cc_start: 0.8134 (m-80) cc_final: 0.7838 (m-80) REVERT: A 257 GLU cc_start: 0.7814 (mp0) cc_final: 0.7266 (mp0) REVERT: A 433 ARG cc_start: 0.5324 (ptt-90) cc_final: 0.4559 (ptp90) REVERT: B 170 ARG cc_start: 0.8340 (tmm-80) cc_final: 0.7471 (mtm110) REVERT: C 143 PHE cc_start: 0.6871 (p90) cc_final: 0.5975 (p90) REVERT: C 186 TRP cc_start: 0.7439 (t-100) cc_final: 0.6912 (t-100) REVERT: D 146 ASN cc_start: 0.8795 (t0) cc_final: 0.8472 (t0) REVERT: D 212 ASP cc_start: 0.8068 (m-30) cc_final: 0.7736 (m-30) REVERT: D 304 TYR cc_start: 0.8633 (OUTLIER) cc_final: 0.8178 (m-80) REVERT: E 91 GLN cc_start: 0.7369 (mm-40) cc_final: 0.7028 (mm110) REVERT: F 188 GLU cc_start: 0.8376 (pm20) cc_final: 0.8146 (mp0) REVERT: F 206 LYS cc_start: 0.8790 (mtmm) cc_final: 0.8492 (mmtt) REVERT: G 105 SER cc_start: 0.9272 (m) cc_final: 0.8964 (p) REVERT: G 185 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7989 (mmt-90) REVERT: G 188 GLU cc_start: 0.8331 (mp0) cc_final: 0.7980 (mm-30) REVERT: G 206 LYS cc_start: 0.8500 (mmmt) cc_final: 0.8086 (mtmt) REVERT: G 320 LYS cc_start: 0.8318 (mmtm) cc_final: 0.7941 (mmtt) REVERT: H 94 ASN cc_start: 0.8440 (p0) cc_final: 0.8039 (p0) REVERT: H 310 GLN cc_start: 0.8616 (tt0) cc_final: 0.8312 (mt0) REVERT: I 34 GLU cc_start: 0.8830 (tt0) cc_final: 0.8446 (tt0) REVERT: I 147 ASP cc_start: 0.8017 (t70) cc_final: 0.7744 (m-30) REVERT: I 348 ASN cc_start: 0.9256 (OUTLIER) cc_final: 0.9025 (t0) REVERT: J 90 ASN cc_start: 0.8311 (t0) cc_final: 0.7916 (t0) REVERT: J 99 HIS cc_start: 0.8287 (OUTLIER) cc_final: 0.7712 (p-80) REVERT: K 82 LYS cc_start: 0.8984 (ttmt) cc_final: 0.8398 (ttmt) REVERT: K 90 ASN cc_start: 0.8829 (t0) cc_final: 0.8512 (t0) REVERT: K 99 HIS cc_start: 0.8368 (OUTLIER) cc_final: 0.6118 (p-80) outliers start: 54 outliers final: 42 residues processed: 280 average time/residue: 0.2042 time to fit residues: 86.0745 Evaluate side-chains 290 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 241 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 153 ARG 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 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 C residue 151 THR Chi-restraints excluded: chain C residue 153 GLN 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 251 ILE Chi-restraints excluded: chain F residue 304 TYR 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 348 ASN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 304 TYR Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 94 ASN Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain I residue 247 SER Chi-restraints excluded: chain I residue 333 ARG Chi-restraints excluded: chain I residue 348 ASN Chi-restraints excluded: chain I residue 355 PHE 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: 4.9990 chunk 267 optimal weight: 1.9990 chunk 240 optimal weight: 0.6980 chunk 249 optimal weight: 0.5980 chunk 67 optimal weight: 7.9990 chunk 270 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 125 optimal weight: 0.0060 chunk 15 optimal weight: 4.9990 chunk 230 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 ASN B 293 HIS C 153 GLN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 ASN J 110 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.141303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.099004 restraints weight = 45306.750| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.83 r_work: 0.2827 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2841 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= 0.114 Angle : 0.640 12.999 33956 Z= 0.298 Chirality : 0.047 0.358 3815 Planarity : 0.004 0.044 4261 Dihedral : 12.039 179.817 3982 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.17 % Allowed : 17.91 % 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: -0.53 (0.15), residues: 2949 helix: 1.68 (0.17), residues: 929 sheet: -0.02 (0.23), residues: 479 loop : -1.85 (0.15), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 64 TYR 0.017 0.001 TYR B 262 PHE 0.022 0.001 PHE D 245 TRP 0.012 0.001 TRP A 394 HIS 0.010 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (24807) covalent geometry : angle 0.64001 / 0.30 (33956) hydrogen bonds : bond 0.02849 / 1.96 ( 995) hydrogen bonds : angle 4.31041 / 3.03 ( 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 301 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 251 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 TRP cc_start: 0.5786 (OUTLIER) cc_final: 0.5022 (p-90) REVERT: A 28 LYS cc_start: 0.7891 (mtpp) cc_final: 0.7679 (pttt) REVERT: A 62 GLN cc_start: 0.7649 (mp10) cc_final: 0.7315 (mp10) REVERT: A 200 HIS cc_start: 0.8284 (t-90) cc_final: 0.7780 (t-90) REVERT: A 228 TRP cc_start: 0.7551 (t-100) cc_final: 0.7111 (t-100) REVERT: A 235 TYR cc_start: 0.8054 (m-80) cc_final: 0.7789 (m-80) REVERT: A 257 GLU cc_start: 0.7765 (mp0) cc_final: 0.7212 (mp0) REVERT: A 433 ARG cc_start: 0.5288 (ptt-90) cc_final: 0.4542 (ptp90) REVERT: B 170 ARG cc_start: 0.8332 (tmm-80) cc_final: 0.7486 (mtm110) REVERT: C 56 GLU cc_start: 0.7780 (pm20) cc_final: 0.7220 (pm20) REVERT: C 143 PHE cc_start: 0.6819 (p90) cc_final: 0.5918 (p90) REVERT: C 186 TRP cc_start: 0.7389 (t-100) cc_final: 0.6852 (t-100) REVERT: D 146 ASN cc_start: 0.8723 (t0) cc_final: 0.8396 (t0) REVERT: D 212 ASP cc_start: 0.7900 (m-30) cc_final: 0.7479 (m-30) REVERT: D 304 TYR cc_start: 0.8594 (OUTLIER) cc_final: 0.8135 (m-80) REVERT: E 91 GLN cc_start: 0.7321 (mm-40) cc_final: 0.6963 (mm110) REVERT: E 99 ASP cc_start: 0.8803 (m-30) cc_final: 0.8518 (m-30) REVERT: F 206 LYS cc_start: 0.8759 (mtmm) cc_final: 0.8504 (mmtt) REVERT: G 105 SER cc_start: 0.9142 (m) cc_final: 0.8875 (p) REVERT: G 185 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7934 (mmt-90) REVERT: G 206 LYS cc_start: 0.8447 (mmmt) cc_final: 0.8105 (mtmt) REVERT: G 320 LYS cc_start: 0.8214 (mmtm) cc_final: 0.7930 (mmtt) REVERT: H 94 ASN cc_start: 0.8325 (p0) cc_final: 0.7968 (p0) REVERT: H 310 GLN cc_start: 0.8506 (tt0) cc_final: 0.8210 (mt0) REVERT: I 34 GLU cc_start: 0.8658 (tt0) cc_final: 0.8283 (tt0) REVERT: I 348 ASN cc_start: 0.9234 (OUTLIER) cc_final: 0.8989 (t0) REVERT: J 90 ASN cc_start: 0.8446 (t0) cc_final: 0.8056 (t0) REVERT: J 99 HIS cc_start: 0.8247 (OUTLIER) cc_final: 0.7658 (p-80) REVERT: K 82 LYS cc_start: 0.8998 (ttmt) cc_final: 0.8438 (ttmt) REVERT: K 90 ASN cc_start: 0.8787 (t0) cc_final: 0.8489 (t0) REVERT: K 99 HIS cc_start: 0.8324 (OUTLIER) cc_final: 0.6151 (p-80) outliers start: 50 outliers final: 39 residues processed: 282 average time/residue: 0.2060 time to fit residues: 87.2488 Evaluate side-chains 285 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 240 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 153 ARG Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 196 THR 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 C residue 151 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 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 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 348 ASN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 304 TYR Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 247 SER Chi-restraints excluded: chain I residue 333 ARG Chi-restraints excluded: chain I residue 348 ASN Chi-restraints excluded: chain I residue 355 PHE 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: 6.9990 chunk 79 optimal weight: 3.9990 chunk 225 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 218 optimal weight: 0.8980 chunk 182 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.0870 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS C 153 GLN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.139381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.097081 restraints weight = 36001.936| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.66 r_work: 0.2840 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24807 Z= 0.163 Angle : 0.666 12.956 33956 Z= 0.309 Chirality : 0.049 0.438 3815 Planarity : 0.004 0.043 4261 Dihedral : 12.084 179.143 3982 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.09 % Allowed : 18.12 % Favored : 79.79 % 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: -0.54 (0.15), residues: 2949 helix: 1.65 (0.17), residues: 925 sheet: -0.06 (0.23), residues: 486 loop : -1.82 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 64 TYR 0.017 0.002 TYR I 304 PHE 0.020 0.001 PHE D 245 TRP 0.013 0.001 TRP A 394 HIS 0.011 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (24807) covalent geometry : angle 0.66601 / 0.31 (33956) hydrogen bonds : bond 0.02989 / 2.06 ( 995) hydrogen bonds : angle 4.37367 / 3.07 ( 2830) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7108.85 seconds wall clock time: 122 minutes 12.10 seconds (7332.10 seconds total)