Starting phenix.real_space_refine on Wed Mar 4 05:01:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n9e_49166/03_2026/9n9e_49166.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n9e_49166/03_2026/9n9e_49166.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n9e_49166/03_2026/9n9e_49166.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n9e_49166/03_2026/9n9e_49166.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n9e_49166/03_2026/9n9e_49166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n9e_49166/03_2026/9n9e_49166.map" } resolution = 2.6 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= 0.024 sd= 0.177 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 8 5.49 5 Mg 3 5.21 5 S 73 5.16 5 C 6710 2.51 5 N 1827 2.21 5 O 2062 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 94 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10685 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3372 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Chain: "B" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3351 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "C" Number of atoms: 3372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3372 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Chain: "S" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 427 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 51} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 92 Unusual residues: {' MG': 2, 'GDP': 1, 'TA1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 1, ' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.08, per 1000 atoms: 0.19 Number of scatterers: 10685 At special positions: 0 Unit cell: (75.21, 73.03, 154.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 73 16.00 P 8 15.00 Mg 3 11.99 O 2062 8.00 N 1827 7.00 C 6710 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 494.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" NE2 HIS A 197 " pdb=" ZN C 503 " pdb="ZN ZN C 503 " - pdb=" NE2 HIS C 197 " 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2492 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 8 sheets defined 55.5% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 48 through 51 removed outlier: 3.738A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 129 removed outlier: 4.190A pdb=" N ILE A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 161 Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.560A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.664A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.767A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.699A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 383 through 402 removed outlier: 4.139A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.791A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 removed outlier: 3.866A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 40 through 48 removed outlier: 4.115A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG B 48 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 110 through 129 removed outlier: 4.293A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 161 Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.584A pdb=" N ASN B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR B 198 " --> pdb=" O LEU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 Processing helix chain 'B' and resid 223 through 239 removed outlier: 3.770A pdb=" N LEU B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 243 Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 324 through 339 Processing helix chain 'B' and resid 384 through 400 removed outlier: 3.635A pdb=" N PHE B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 390 " --> pdb=" O GLU B 386 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG B 400 " --> pdb=" O THR B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.981A pdb=" N TYR B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 435 removed outlier: 3.747A pdb=" N PHE B 418 " --> pdb=" O ASP B 414 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 29 Processing helix chain 'C' and resid 48 through 51 removed outlier: 3.737A pdb=" N THR C 51 " --> pdb=" O SER C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 48 through 51' Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 110 through 129 removed outlier: 4.190A pdb=" N ILE C 114 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ASP C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LEU C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 removed outlier: 4.636A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.560A pdb=" N ASN C 186 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N HIS C 192 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N THR C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 216 Processing helix chain 'C' and resid 223 through 244 removed outlier: 3.665A pdb=" N LEU C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 277 through 283 removed outlier: 3.766A pdb=" N HIS C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.700A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 338 Processing helix chain 'C' and resid 383 through 402 removed outlier: 4.139A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TRP C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA C 400 " --> pdb=" O ASP C 396 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.791A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 437 removed outlier: 3.866A pdb=" N PHE C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'S' and resid 222 through 273 Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.298A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLU A 3 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N LEU A 136 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE A 5 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N PHE A 138 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE A 7 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N SER A 140 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N VAL A 9 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.548A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 92 through 94 removed outlier: 8.292A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLU B 3 " --> pdb=" O GLY B 134 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N GLN B 136 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL B 5 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N THR B 138 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE B 7 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N SER B 140 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ALA B 9 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ASN B 167 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N PHE B 135 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL B 171 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N HIS B 139 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N MET B 166 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N TYR B 202 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THR B 168 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE B 204 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N SER B 170 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ASP B 205 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 12.023A pdb=" N PHE B 272 " --> pdb=" O ASP B 205 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N SER B 374 " --> pdb=" O PHE B 319 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE B 319 " --> pdb=" O SER B 374 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR B 376 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ALA B 317 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE B 378 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL B 315 " --> pdb=" O ILE B 378 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASN B 380 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA6, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.298A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLU C 3 " --> pdb=" O GLY C 134 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N LEU C 136 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE C 5 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N PHE C 138 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE C 7 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N SER C 140 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N VAL C 9 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N GLN C 133 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU C 167 " --> pdb=" O GLN C 133 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N PHE C 135 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N PHE C 169 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N VAL C 137 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ILE C 171 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N HIS C 139 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS C 200 " --> pdb=" O LYS C 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA8, first strand: chain 'C' and resid 269 through 273 removed outlier: 3.549A pdb=" N ALA C 314 " --> pdb=" O ASN C 380 " (cutoff:3.500A) 540 hydrogen bonds defined for protein. 1572 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.14 Time building geometry restraints manager: 1.09 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: 1968 1.32 - 1.45: 2790 1.45 - 1.57: 6029 1.57 - 1.69: 17 1.69 - 1.81: 114 Bond restraints: 10918 Sorted by residual: bond pdb=" CA SER B 324 " pdb=" CB SER B 324 " ideal model delta sigma weight residual 1.529 1.478 0.051 1.53e-02 4.27e+03 1.09e+01 bond pdb=" CA PHE B 319 " pdb=" C PHE B 319 " ideal model delta sigma weight residual 1.523 1.482 0.041 1.24e-02 6.50e+03 1.07e+01 bond pdb=" N VAL B 315 " pdb=" CA VAL B 315 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.19e-02 7.06e+03 9.51e+00 bond pdb=" N VAL B 328 " pdb=" CA VAL B 328 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.21e-02 6.83e+03 9.27e+00 bond pdb=" N ASN B 339 " pdb=" CA ASN B 339 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.10e-02 8.26e+03 9.07e+00 ... (remaining 10913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 13794 1.36 - 2.72: 845 2.72 - 4.08: 148 4.08 - 5.43: 27 5.43 - 6.79: 15 Bond angle restraints: 14829 Sorted by residual: angle pdb=" N GLY B 134 " pdb=" CA GLY B 134 " pdb=" C GLY B 134 " ideal model delta sigma weight residual 111.09 117.84 -6.75 1.33e+00 5.65e-01 2.58e+01 angle pdb=" CA GLY B 321 " pdb=" C GLY B 321 " pdb=" O GLY B 321 " ideal model delta sigma weight residual 122.16 118.28 3.88 8.20e-01 1.49e+00 2.24e+01 angle pdb=" CA PHE B 319 " pdb=" CB PHE B 319 " pdb=" CG PHE B 319 " ideal model delta sigma weight residual 113.80 118.42 -4.62 1.00e+00 1.00e+00 2.13e+01 angle pdb=" CA ALA B 316 " pdb=" C ALA B 316 " pdb=" N ALA B 317 " ideal model delta sigma weight residual 116.28 121.77 -5.49 1.26e+00 6.30e-01 1.90e+01 angle pdb=" CA GLY C 10 " pdb=" C GLY C 10 " pdb=" O GLY C 10 " ideal model delta sigma weight residual 122.59 118.35 4.24 1.04e+00 9.25e-01 1.66e+01 ... (remaining 14824 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 6404 35.93 - 71.85: 143 71.85 - 107.78: 27 107.78 - 143.71: 14 143.71 - 179.63: 5 Dihedral angle restraints: 6593 sinusoidal: 2716 harmonic: 3877 Sorted by residual: dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -110.36 179.63 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTP C 501 " pdb=" O5' GTP C 501 " pdb=" PA GTP C 501 " pdb=" O3A GTP C 501 " ideal model delta sinusoidal sigma weight residual 69.27 -117.48 -173.25 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -39.18 143.77 1 2.00e+01 2.50e-03 4.34e+01 ... (remaining 6590 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1100 0.040 - 0.080: 353 0.080 - 0.119: 137 0.119 - 0.159: 21 0.159 - 0.199: 9 Chirality restraints: 1620 Sorted by residual: chirality pdb=" CA PHE B 319 " pdb=" N PHE B 319 " pdb=" C PHE B 319 " pdb=" CB PHE B 319 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" C10 TA1 B 504 " pdb=" C02 TA1 B 504 " pdb=" C11 TA1 B 504 " pdb=" C18 TA1 B 504 " both_signs ideal model delta sigma weight residual False 2.54 2.35 0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CA ILE C 16 " pdb=" N ILE C 16 " pdb=" C ILE C 16 " pdb=" CB ILE C 16 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.68e-01 ... (remaining 1617 not shown) Planarity restraints: 1926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 311 " 0.189 9.50e-02 1.11e+02 8.47e-02 4.46e+00 pdb=" NE ARG B 311 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 311 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B 311 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 311 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 308 " 0.163 9.50e-02 1.11e+02 7.32e-02 3.29e+00 pdb=" NE ARG B 308 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG B 308 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B 308 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 308 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 71 " -0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO A 72 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " -0.025 5.00e-02 4.00e+02 ... (remaining 1923 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.42: 29 2.42 - 3.04: 6743 3.04 - 3.66: 15722 3.66 - 4.28: 24158 4.28 - 4.90: 41715 Nonbonded interactions: 88367 Sorted by model distance: nonbonded pdb="MG MG C 502 " pdb=" O HOH C 601 " model vdw 1.805 2.170 nonbonded pdb="MG MG C 502 " pdb=" O HOH C 602 " model vdw 1.904 2.170 nonbonded pdb=" O1B GTP C 501 " pdb="MG MG C 502 " model vdw 2.176 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG B 501 " model vdw 2.188 2.170 nonbonded pdb=" OD2 ASP C 46 " pdb=" OG SER C 48 " model vdw 2.237 3.040 ... (remaining 88362 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 501) selection = (chain 'C' and resid 1 through 501) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.150 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 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 : 0.006 0.271 10920 Z= 0.338 Angle : 0.749 6.792 14829 Z= 0.522 Chirality : 0.047 0.199 1620 Planarity : 0.006 0.085 1926 Dihedral : 17.935 179.632 4101 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.18 % Allowed : 9.60 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.92 % 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: 1.81 (0.23), residues: 1327 helix: 2.03 (0.21), residues: 628 sheet: 1.94 (0.35), residues: 204 loop : -0.19 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 123 TYR 0.008 0.001 TYR B 61 PHE 0.018 0.001 PHE B 319 TRP 0.010 0.001 TRP A 21 HIS 0.005 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00494 (10918) covalent geometry : angle 0.74878 (14829) hydrogen bonds : bond 0.15185 ( 540) hydrogen bonds : angle 5.72438 ( 1572) metal coordination : bond 0.26839 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: B 205 ASP cc_start: 0.8338 (t0) cc_final: 0.8128 (t0) REVERT: B 283 TYR cc_start: 0.7911 (m-80) cc_final: 0.6672 (t80) REVERT: B 420 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8656 (mm-30) REVERT: C 50 ASN cc_start: 0.8837 (t0) cc_final: 0.8512 (t0) outliers start: 2 outliers final: 0 residues processed: 99 average time/residue: 0.7687 time to fit residues: 80.7123 Evaluate side-chains 75 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS A 15 GLN A 18 ASN A 35 GLN A 61 HIS A 192 HIS A 258 ASN B 37 HIS B 101 ASN B 433 GLN C 8 HIS C 15 GLN C 18 ASN C 31 GLN C 192 HIS C 258 ASN S 261 GLN S 266 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.092280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.069867 restraints weight = 17638.213| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.66 r_work: 0.3021 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 10920 Z= 0.268 Angle : 0.663 9.323 14829 Z= 0.344 Chirality : 0.048 0.185 1620 Planarity : 0.005 0.045 1926 Dihedral : 15.500 178.891 1603 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.00 % Allowed : 9.78 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.92 % 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: 1.71 (0.23), residues: 1327 helix: 2.05 (0.20), residues: 637 sheet: 1.71 (0.35), residues: 194 loop : -0.32 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 308 TYR 0.018 0.002 TYR B 312 PHE 0.019 0.002 PHE A 255 TRP 0.016 0.002 TRP C 21 HIS 0.006 0.002 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00642 (10918) covalent geometry : angle 0.66265 (14829) hydrogen bonds : bond 0.07502 ( 540) hydrogen bonds : angle 4.40730 ( 1572) metal coordination : bond 0.00519 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 84 ARG cc_start: 0.7844 (ptm160) cc_final: 0.7307 (ptp90) REVERT: A 154 MET cc_start: 0.8944 (mmm) cc_final: 0.8672 (tpp) REVERT: A 377 MET cc_start: 0.9233 (OUTLIER) cc_final: 0.8480 (tmm) REVERT: A 425 MET cc_start: 0.8768 (tpt) cc_final: 0.8323 (tpt) REVERT: A 433 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8085 (pp20) REVERT: B 133 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8512 (tp40) REVERT: B 205 ASP cc_start: 0.8433 (t0) cc_final: 0.8115 (t0) REVERT: B 283 TYR cc_start: 0.8064 (m-80) cc_final: 0.6677 (t80) REVERT: B 308 ARG cc_start: 0.8381 (ptp-110) cc_final: 0.7993 (mtm-85) REVERT: B 416 MET cc_start: 0.8292 (mpm) cc_final: 0.7857 (mpm) REVERT: C 50 ASN cc_start: 0.8735 (t0) cc_final: 0.8401 (t160) REVERT: C 56 THR cc_start: 0.8289 (OUTLIER) cc_final: 0.7974 (p) REVERT: C 203 MET cc_start: 0.9357 (OUTLIER) cc_final: 0.8709 (mmt) REVERT: C 302 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8636 (mmm) REVERT: C 367 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7872 (m-30) outliers start: 34 outliers final: 9 residues processed: 103 average time/residue: 0.6708 time to fit residues: 73.7915 Evaluate side-chains 92 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 367 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 29 optimal weight: 6.9990 chunk 127 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 0.3980 chunk 100 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 HIS B 37 HIS B 91 ASN C 35 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.094446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.071859 restraints weight = 17611.082| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.68 r_work: 0.3067 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10920 Z= 0.155 Angle : 0.559 9.861 14829 Z= 0.284 Chirality : 0.045 0.386 1620 Planarity : 0.004 0.040 1926 Dihedral : 13.127 179.806 1603 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.47 % Allowed : 10.84 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.92 % 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: 1.81 (0.23), residues: 1327 helix: 2.20 (0.20), residues: 639 sheet: 1.52 (0.35), residues: 201 loop : -0.30 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 278 TYR 0.010 0.001 TYR A 161 PHE 0.018 0.001 PHE A 255 TRP 0.016 0.002 TRP C 21 HIS 0.011 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00359 (10918) covalent geometry : angle 0.55899 (14829) hydrogen bonds : bond 0.05831 ( 540) hydrogen bonds : angle 4.08985 ( 1572) metal coordination : bond 0.00258 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 154 MET cc_start: 0.8918 (mmm) cc_final: 0.8622 (tpp) REVERT: A 425 MET cc_start: 0.8713 (tpt) cc_final: 0.8264 (tpt) REVERT: B 133 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8649 (tp40) REVERT: B 160 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7738 (tm-30) REVERT: B 205 ASP cc_start: 0.8436 (t0) cc_final: 0.8074 (t0) REVERT: B 283 TYR cc_start: 0.8070 (m-80) cc_final: 0.6675 (t80) REVERT: B 308 ARG cc_start: 0.8423 (ptp-110) cc_final: 0.8122 (mtm180) REVERT: B 416 MET cc_start: 0.8249 (mpm) cc_final: 0.7731 (mpm) REVERT: B 420 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7975 (mm-30) REVERT: C 56 THR cc_start: 0.8337 (OUTLIER) cc_final: 0.8021 (p) REVERT: C 282 TYR cc_start: 0.8291 (OUTLIER) cc_final: 0.8061 (m-80) REVERT: C 302 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8500 (mtm) REVERT: C 367 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7900 (m-30) outliers start: 28 outliers final: 8 residues processed: 98 average time/residue: 0.6925 time to fit residues: 72.3714 Evaluate side-chains 88 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 391 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 42 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.094594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.072128 restraints weight = 17760.099| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.67 r_work: 0.3069 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10920 Z= 0.146 Angle : 0.541 9.406 14829 Z= 0.276 Chirality : 0.045 0.365 1620 Planarity : 0.004 0.039 1926 Dihedral : 11.980 178.336 1603 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.73 % Allowed : 11.45 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.92 % 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: 1.77 (0.23), residues: 1327 helix: 2.24 (0.21), residues: 641 sheet: 1.41 (0.34), residues: 206 loop : -0.39 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 84 TYR 0.010 0.001 TYR A 83 PHE 0.016 0.001 PHE A 255 TRP 0.015 0.001 TRP C 21 HIS 0.004 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00336 (10918) covalent geometry : angle 0.54068 (14829) hydrogen bonds : bond 0.05517 ( 540) hydrogen bonds : angle 3.98068 ( 1572) metal coordination : bond 0.00149 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 79 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 154 MET cc_start: 0.8945 (mmm) cc_final: 0.8621 (tpp) REVERT: A 203 MET cc_start: 0.9529 (OUTLIER) cc_final: 0.8632 (mmm) REVERT: A 377 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.8716 (tmm) REVERT: A 425 MET cc_start: 0.8707 (tpt) cc_final: 0.8259 (tpt) REVERT: A 432 TYR cc_start: 0.8869 (OUTLIER) cc_final: 0.7021 (t80) REVERT: A 433 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8056 (pp20) REVERT: B 133 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8732 (tp40) REVERT: B 160 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7756 (tm-30) REVERT: B 205 ASP cc_start: 0.8438 (t0) cc_final: 0.8053 (t0) REVERT: B 283 TYR cc_start: 0.8069 (m-80) cc_final: 0.6654 (t80) REVERT: B 308 ARG cc_start: 0.8438 (ptp-110) cc_final: 0.8228 (mtm-85) REVERT: B 416 MET cc_start: 0.8304 (mpm) cc_final: 0.7715 (mpm) REVERT: B 420 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8042 (mm-30) REVERT: C 56 THR cc_start: 0.8212 (OUTLIER) cc_final: 0.7854 (p) REVERT: C 282 TYR cc_start: 0.8322 (OUTLIER) cc_final: 0.8089 (m-80) REVERT: C 302 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8498 (mtm) REVERT: C 367 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7915 (m-30) outliers start: 31 outliers final: 15 residues processed: 101 average time/residue: 0.6832 time to fit residues: 73.7559 Evaluate side-chains 103 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 391 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 119 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 60 optimal weight: 20.0000 chunk 93 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 115 optimal weight: 0.8980 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS B 101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.091257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.068881 restraints weight = 17748.828| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.65 r_work: 0.3005 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 10920 Z= 0.249 Angle : 0.597 7.232 14829 Z= 0.312 Chirality : 0.048 0.303 1620 Planarity : 0.004 0.041 1926 Dihedral : 12.153 178.662 1603 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.44 % Allowed : 11.28 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.23), residues: 1327 helix: 2.03 (0.21), residues: 638 sheet: 1.25 (0.35), residues: 202 loop : -0.53 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 339 TYR 0.012 0.002 TYR A 161 PHE 0.018 0.002 PHE A 255 TRP 0.015 0.002 TRP C 21 HIS 0.006 0.002 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00603 (10918) covalent geometry : angle 0.59692 (14829) hydrogen bonds : bond 0.07114 ( 540) hydrogen bonds : angle 4.19785 ( 1572) metal coordination : bond 0.00216 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 79 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 154 MET cc_start: 0.9006 (mmm) cc_final: 0.8733 (tpp) REVERT: A 203 MET cc_start: 0.9543 (OUTLIER) cc_final: 0.8646 (mmm) REVERT: A 377 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8804 (tmm) REVERT: A 433 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8106 (pp20) REVERT: B 160 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7697 (tm-30) REVERT: B 205 ASP cc_start: 0.8513 (t0) cc_final: 0.8181 (t0) REVERT: B 283 TYR cc_start: 0.8146 (m-80) cc_final: 0.6632 (t80) REVERT: B 416 MET cc_start: 0.8391 (mpm) cc_final: 0.7856 (mpm) REVERT: B 420 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8116 (mm-30) REVERT: C 56 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.7999 (p) REVERT: C 302 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8597 (mmm) REVERT: C 367 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7875 (m-30) REVERT: S 255 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7185 (mpp) outliers start: 39 outliers final: 18 residues processed: 108 average time/residue: 0.6835 time to fit residues: 78.8745 Evaluate side-chains 103 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain S residue 255 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 82 optimal weight: 0.9990 chunk 3 optimal weight: 0.0670 chunk 113 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN B 37 HIS B 101 ASN B 294 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.095341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.072849 restraints weight = 17847.560| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.68 r_work: 0.3085 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10920 Z= 0.116 Angle : 0.529 9.286 14829 Z= 0.269 Chirality : 0.043 0.251 1620 Planarity : 0.004 0.046 1926 Dihedral : 11.718 177.167 1603 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.47 % Allowed : 12.51 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.92 % 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: 1.78 (0.24), residues: 1327 helix: 2.31 (0.21), residues: 640 sheet: 1.36 (0.35), residues: 201 loop : -0.45 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 308 TYR 0.010 0.001 TYR A 161 PHE 0.016 0.001 PHE A 255 TRP 0.017 0.002 TRP C 21 HIS 0.021 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00251 (10918) covalent geometry : angle 0.52939 (14829) hydrogen bonds : bond 0.04940 ( 540) hydrogen bonds : angle 3.91905 ( 1572) metal coordination : bond 0.00090 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 84 ARG cc_start: 0.7473 (ptp90) cc_final: 0.7053 (ptp90) REVERT: A 133 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7852 (mt0) REVERT: A 154 MET cc_start: 0.8982 (mmm) cc_final: 0.8653 (tpp) REVERT: A 203 MET cc_start: 0.9515 (OUTLIER) cc_final: 0.8599 (mmm) REVERT: A 377 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8638 (tmm) REVERT: A 425 MET cc_start: 0.8691 (tpt) cc_final: 0.8271 (tpt) REVERT: A 432 TYR cc_start: 0.8835 (OUTLIER) cc_final: 0.7223 (t80) REVERT: B 160 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: B 205 ASP cc_start: 0.8424 (t0) cc_final: 0.8089 (t0) REVERT: B 283 TYR cc_start: 0.8104 (m-80) cc_final: 0.6617 (t80) REVERT: B 416 MET cc_start: 0.8369 (mpm) cc_final: 0.7819 (mpm) REVERT: B 420 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8084 (mm-30) REVERT: B 424 ASN cc_start: 0.8846 (t0) cc_final: 0.8613 (t0) REVERT: C 203 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.8396 (mmt) REVERT: C 367 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7872 (m-30) outliers start: 28 outliers final: 13 residues processed: 100 average time/residue: 0.6774 time to fit residues: 72.4705 Evaluate side-chains 98 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 435 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 132 optimal weight: 30.0000 chunk 98 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS B 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.091273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.068862 restraints weight = 17930.482| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.65 r_work: 0.3005 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 10920 Z= 0.252 Angle : 0.616 10.605 14829 Z= 0.318 Chirality : 0.047 0.259 1620 Planarity : 0.004 0.042 1926 Dihedral : 11.912 178.995 1603 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.73 % Allowed : 12.60 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.23), residues: 1327 helix: 2.08 (0.21), residues: 638 sheet: 1.23 (0.35), residues: 201 loop : -0.58 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 339 TYR 0.011 0.002 TYR A 161 PHE 0.017 0.002 PHE A 255 TRP 0.013 0.002 TRP C 21 HIS 0.006 0.002 HIS C 28 Details of bonding type rmsd covalent geometry : bond 0.00609 (10918) covalent geometry : angle 0.61554 (14829) hydrogen bonds : bond 0.06910 ( 540) hydrogen bonds : angle 4.14392 ( 1572) metal coordination : bond 0.00223 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 77 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 154 MET cc_start: 0.9022 (mmm) cc_final: 0.8711 (tpp) REVERT: A 203 MET cc_start: 0.9546 (OUTLIER) cc_final: 0.8635 (mmm) REVERT: A 377 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8821 (tmm) REVERT: A 432 TYR cc_start: 0.8899 (OUTLIER) cc_final: 0.6991 (t80) REVERT: A 433 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8045 (pp20) REVERT: B 160 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7678 (tm-30) REVERT: B 205 ASP cc_start: 0.8534 (t0) cc_final: 0.8168 (t0) REVERT: B 283 TYR cc_start: 0.8090 (m-80) cc_final: 0.6609 (t80) REVERT: B 416 MET cc_start: 0.8409 (mpm) cc_final: 0.7980 (mpm) REVERT: B 420 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8189 (mm-30) REVERT: C 203 MET cc_start: 0.9310 (OUTLIER) cc_final: 0.8449 (mmt) REVERT: C 367 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7891 (m-30) REVERT: S 255 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7035 (mpp) outliers start: 31 outliers final: 16 residues processed: 101 average time/residue: 0.6278 time to fit residues: 68.2154 Evaluate side-chains 100 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain S residue 255 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 75 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 3 optimal weight: 0.2980 chunk 95 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS B 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.094234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.071619 restraints weight = 17724.789| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.68 r_work: 0.3062 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10920 Z= 0.132 Angle : 0.546 9.892 14829 Z= 0.275 Chirality : 0.044 0.233 1620 Planarity : 0.004 0.039 1926 Dihedral : 11.645 177.644 1603 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.38 % Allowed : 13.04 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.92 % 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: 1.71 (0.23), residues: 1327 helix: 2.27 (0.21), residues: 640 sheet: 1.29 (0.35), residues: 201 loop : -0.48 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 322 TYR 0.010 0.001 TYR A 161 PHE 0.017 0.001 PHE A 255 TRP 0.017 0.002 TRP C 21 HIS 0.008 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00299 (10918) covalent geometry : angle 0.54552 (14829) hydrogen bonds : bond 0.05290 ( 540) hydrogen bonds : angle 3.94283 ( 1572) metal coordination : bond 0.00112 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7713 (mmm) cc_final: 0.6896 (ttt) REVERT: A 154 MET cc_start: 0.9010 (mmm) cc_final: 0.8703 (tpp) REVERT: A 203 MET cc_start: 0.9532 (OUTLIER) cc_final: 0.8622 (mmm) REVERT: A 377 MET cc_start: 0.9241 (OUTLIER) cc_final: 0.8718 (tmm) REVERT: A 392 ASP cc_start: 0.8177 (m-30) cc_final: 0.7973 (m-30) REVERT: A 425 MET cc_start: 0.8698 (tpt) cc_final: 0.8285 (tpt) REVERT: A 432 TYR cc_start: 0.8848 (OUTLIER) cc_final: 0.7133 (t80) REVERT: B 160 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7673 (tm-30) REVERT: B 205 ASP cc_start: 0.8446 (t0) cc_final: 0.8094 (t0) REVERT: B 283 TYR cc_start: 0.8015 (m-80) cc_final: 0.6625 (t80) REVERT: B 416 MET cc_start: 0.8425 (mpm) cc_final: 0.8020 (mpm) REVERT: B 420 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8161 (mm-30) REVERT: B 424 ASN cc_start: 0.8845 (t0) cc_final: 0.8591 (t0) REVERT: C 56 THR cc_start: 0.8217 (OUTLIER) cc_final: 0.7834 (p) REVERT: C 203 MET cc_start: 0.9293 (OUTLIER) cc_final: 0.8411 (mmt) REVERT: C 284 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8339 (mt-10) REVERT: C 367 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7849 (m-30) outliers start: 27 outliers final: 14 residues processed: 103 average time/residue: 0.5954 time to fit residues: 66.0142 Evaluate side-chains 102 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 435 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 90 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 116 optimal weight: 0.8980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS B 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.093239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.070689 restraints weight = 17742.501| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.67 r_work: 0.3040 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10920 Z= 0.168 Angle : 0.564 10.926 14829 Z= 0.287 Chirality : 0.044 0.231 1620 Planarity : 0.004 0.039 1926 Dihedral : 11.593 177.748 1603 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.20 % Allowed : 13.74 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.92 % 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: 1.70 (0.23), residues: 1327 helix: 2.26 (0.21), residues: 638 sheet: 1.22 (0.34), residues: 206 loop : -0.47 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 322 TYR 0.010 0.001 TYR A 161 PHE 0.016 0.001 PHE A 255 TRP 0.013 0.001 TRP C 21 HIS 0.004 0.001 HIS C 28 Details of bonding type rmsd covalent geometry : bond 0.00399 (10918) covalent geometry : angle 0.56442 (14829) hydrogen bonds : bond 0.05764 ( 540) hydrogen bonds : angle 3.98678 ( 1572) metal coordination : bond 0.00182 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 154 MET cc_start: 0.9028 (mmm) cc_final: 0.8697 (tpp) REVERT: A 203 MET cc_start: 0.9535 (OUTLIER) cc_final: 0.8627 (mmm) REVERT: A 377 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.8760 (tmm) REVERT: A 425 MET cc_start: 0.8707 (tpt) cc_final: 0.8296 (tpt) REVERT: A 432 TYR cc_start: 0.8866 (OUTLIER) cc_final: 0.7147 (t80) REVERT: B 1 MET cc_start: 0.7900 (tpt) cc_final: 0.7694 (tpp) REVERT: B 160 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7644 (tm-30) REVERT: B 205 ASP cc_start: 0.8482 (t0) cc_final: 0.8123 (t0) REVERT: B 283 TYR cc_start: 0.7946 (m-80) cc_final: 0.6598 (t80) REVERT: B 416 MET cc_start: 0.8464 (mpm) cc_final: 0.8021 (mpm) REVERT: B 420 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8190 (mm-30) REVERT: B 424 ASN cc_start: 0.8855 (t0) cc_final: 0.8551 (t160) REVERT: C 56 THR cc_start: 0.8235 (OUTLIER) cc_final: 0.7854 (p) REVERT: C 120 ASP cc_start: 0.8258 (m-30) cc_final: 0.7810 (m-30) REVERT: C 203 MET cc_start: 0.9301 (OUTLIER) cc_final: 0.8434 (mmt) REVERT: C 367 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7869 (m-30) outliers start: 25 outliers final: 16 residues processed: 100 average time/residue: 0.6179 time to fit residues: 66.5501 Evaluate side-chains 104 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 391 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 56 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 116 optimal weight: 0.0980 chunk 126 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 73 optimal weight: 8.9990 chunk 115 optimal weight: 0.8980 chunk 120 optimal weight: 0.0770 chunk 50 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS B 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.096157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.073681 restraints weight = 17765.818| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.69 r_work: 0.3102 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10920 Z= 0.108 Angle : 0.534 11.428 14829 Z= 0.267 Chirality : 0.043 0.215 1620 Planarity : 0.004 0.039 1926 Dihedral : 11.260 173.130 1603 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.94 % Allowed : 13.83 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.92 % 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: 1.88 (0.24), residues: 1327 helix: 2.41 (0.21), residues: 641 sheet: 1.36 (0.35), residues: 205 loop : -0.43 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 278 TYR 0.010 0.001 TYR B 36 PHE 0.015 0.001 PHE A 255 TRP 0.020 0.002 TRP C 21 HIS 0.007 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00229 (10918) covalent geometry : angle 0.53439 (14829) hydrogen bonds : bond 0.04534 ( 540) hydrogen bonds : angle 3.86821 ( 1572) metal coordination : bond 0.00053 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7600 (mmm) cc_final: 0.6699 (ttt) REVERT: A 84 ARG cc_start: 0.7298 (ptp90) cc_final: 0.7008 (ptp90) REVERT: A 154 MET cc_start: 0.9020 (mmm) cc_final: 0.8675 (tpp) REVERT: A 377 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8594 (tmm) REVERT: A 392 ASP cc_start: 0.8125 (m-30) cc_final: 0.7923 (m-30) REVERT: A 425 MET cc_start: 0.8647 (tpt) cc_final: 0.8251 (tpt) REVERT: A 432 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.7291 (t80) REVERT: B 160 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7673 (tm-30) REVERT: B 205 ASP cc_start: 0.8415 (t0) cc_final: 0.8066 (t0) REVERT: B 283 TYR cc_start: 0.7988 (m-80) cc_final: 0.6591 (t80) REVERT: B 416 MET cc_start: 0.8421 (mpm) cc_final: 0.7999 (mpm) REVERT: B 420 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8175 (mm-30) REVERT: B 424 ASN cc_start: 0.8793 (t0) cc_final: 0.8568 (t0) REVERT: C 203 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.8384 (mmt) REVERT: C 284 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8331 (mt-10) REVERT: C 367 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7846 (m-30) outliers start: 22 outliers final: 12 residues processed: 99 average time/residue: 0.6752 time to fit residues: 71.3858 Evaluate side-chains 98 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 391 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 97 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 101 ASN B 101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.092594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.070191 restraints weight = 17940.800| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.66 r_work: 0.3032 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 10920 Z= 0.204 Angle : 0.583 10.205 14829 Z= 0.298 Chirality : 0.045 0.220 1620 Planarity : 0.004 0.040 1926 Dihedral : 11.468 173.976 1603 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.85 % Allowed : 13.92 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.92 % 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: 1.75 (0.23), residues: 1327 helix: 2.29 (0.21), residues: 638 sheet: 1.25 (0.35), residues: 206 loop : -0.44 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 339 TYR 0.010 0.001 TYR A 161 PHE 0.016 0.002 PHE A 255 TRP 0.010 0.002 TRP C 21 HIS 0.007 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00491 (10918) covalent geometry : angle 0.58336 (14829) hydrogen bonds : bond 0.06077 ( 540) hydrogen bonds : angle 3.99863 ( 1572) metal coordination : bond 0.00218 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3023.26 seconds wall clock time: 52 minutes 21.56 seconds (3141.56 seconds total)