Starting phenix.real_space_refine on Wed Mar 4 12:00:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qqk_14122/03_2026/7qqk_14122.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qqk_14122/03_2026/7qqk_14122.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qqk_14122/03_2026/7qqk_14122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qqk_14122/03_2026/7qqk_14122.map" model { file = "/net/cci-nas-00/data/ceres_data/7qqk_14122/03_2026/7qqk_14122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qqk_14122/03_2026/7qqk_14122.cif" } resolution = 3.8 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= 0.002 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 32 5.16 5 C 8356 2.51 5 N 2476 2.21 5 O 2568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 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: 13444 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3295 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 399} Chain: "B" Number of atoms: 3295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3295 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 399} Chain: "C" Number of atoms: 3295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3295 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 399} Chain: "D" Number of atoms: 3295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3295 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 399} Chain: "E" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Chain: "F" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Chain: "G" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Chain: "H" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Time building chain proxies: 3.25, per 1000 atoms: 0.24 Number of scatterers: 13444 At special positions: 0 Unit cell: (122.631, 152.541, 83.748, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 12 15.00 O 2568 8.00 N 2476 7.00 C 8356 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 530.8 milliseconds 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3224 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 15 sheets defined 41.9% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 removed outlier: 3.873A pdb=" N ALA A 5 " --> pdb=" O PRO A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 36 removed outlier: 3.703A pdb=" N ILE A 22 " --> pdb=" O HIS A 18 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU A 24 " --> pdb=" O ASP A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 46 Processing helix chain 'A' and resid 50 through 62 removed outlier: 3.871A pdb=" N GLY A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 75 removed outlier: 3.915A pdb=" N ALA A 75 " --> pdb=" O PRO A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 83 removed outlier: 3.532A pdb=" N GLU A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 95 Processing helix chain 'A' and resid 116 through 123 removed outlier: 3.797A pdb=" N ARG A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 164 Proline residue: A 159 - end of helix Processing helix chain 'A' and resid 202 through 213 Processing helix chain 'A' and resid 214 through 224 removed outlier: 3.959A pdb=" N ASP A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY A 224 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 246 removed outlier: 3.552A pdb=" N ILE A 246 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 321 Processing helix chain 'A' and resid 342 through 361 removed outlier: 3.730A pdb=" N ASN A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'B' and resid 17 through 36 Processing helix chain 'B' and resid 50 through 62 removed outlier: 3.675A pdb=" N GLY B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 77 Processing helix chain 'B' and resid 77 through 83 removed outlier: 3.789A pdb=" N ARG B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 95 Processing helix chain 'B' and resid 116 through 123 removed outlier: 4.008A pdb=" N ARG B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 removed outlier: 3.941A pdb=" N SER B 131 " --> pdb=" O PRO B 127 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 127 through 132' Processing helix chain 'B' and resid 138 through 164 Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 202 through 214 removed outlier: 4.386A pdb=" N GLN B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 224 removed outlier: 3.732A pdb=" N ASP B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 246 Processing helix chain 'B' and resid 310 through 321 Processing helix chain 'B' and resid 339 through 361 Processing helix chain 'B' and resid 373 through 384 Processing helix chain 'C' and resid 2 through 6 removed outlier: 3.711A pdb=" N ALA C 5 " --> pdb=" O PRO C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 36 removed outlier: 4.386A pdb=" N ALA C 23 " --> pdb=" O SER C 19 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU C 24 " --> pdb=" O ASP C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 62 removed outlier: 3.654A pdb=" N GLY C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 77 Processing helix chain 'C' and resid 83 through 95 removed outlier: 3.526A pdb=" N ARG C 87 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 123 removed outlier: 4.390A pdb=" N ASP C 119 " --> pdb=" O TYR C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 132 removed outlier: 3.759A pdb=" N SER C 131 " --> pdb=" O PRO C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 164 Proline residue: C 159 - end of helix Processing helix chain 'C' and resid 179 through 183 removed outlier: 3.717A pdb=" N ASP C 182 " --> pdb=" O GLN C 179 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG C 183 " --> pdb=" O VAL C 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 179 through 183' Processing helix chain 'C' and resid 202 through 213 Processing helix chain 'C' and resid 215 through 224 Processing helix chain 'C' and resid 235 through 246 Processing helix chain 'C' and resid 309 through 321 removed outlier: 4.508A pdb=" N PHE C 313 " --> pdb=" O SER C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 361 Processing helix chain 'C' and resid 373 through 384 removed outlier: 3.539A pdb=" N THR C 384 " --> pdb=" O ILE C 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 35 Processing helix chain 'D' and resid 50 through 61 removed outlier: 3.599A pdb=" N ARG D 54 " --> pdb=" O ASP D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 77 Processing helix chain 'D' and resid 78 through 83 removed outlier: 3.522A pdb=" N GLU D 82 " --> pdb=" O ARG D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 95 Processing helix chain 'D' and resid 116 through 123 removed outlier: 4.040A pdb=" N ARG D 120 " --> pdb=" O ASP D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 164 Proline residue: D 159 - end of helix Processing helix chain 'D' and resid 179 through 183 removed outlier: 3.635A pdb=" N ARG D 183 " --> pdb=" O VAL D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 214 removed outlier: 4.332A pdb=" N GLN D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 224 removed outlier: 3.941A pdb=" N ASP D 218 " --> pdb=" O GLN D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 246 Processing helix chain 'D' and resid 309 through 321 removed outlier: 4.091A pdb=" N PHE D 313 " --> pdb=" O SER D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 361 Processing helix chain 'D' and resid 373 through 384 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 6.560A pdb=" N VAL A 12 " --> pdb=" O TRP A 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 70 removed outlier: 3.672A pdb=" N VAL A 103 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N LYS A 135 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE A 102 " --> pdb=" O LYS A 135 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 188 through 191 removed outlier: 8.514A pdb=" N LEU A 188 " --> pdb=" O GLU A 167 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG A 169 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE A 190 " --> pdb=" O ARG A 169 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N SER A 171 " --> pdb=" O ILE A 190 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 255 through 257 Processing sheet with id=AA5, first strand: chain 'A' and resid 278 through 283 removed outlier: 7.385A pdb=" N HIS A 329 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N GLU A 283 " --> pdb=" O TRP A 327 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N TRP A 327 " --> pdb=" O GLU A 283 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA A 326 " --> pdb=" O ASP A 297 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 299 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL A 366 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR A 392 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU A 368 " --> pdb=" O TYR A 392 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N TRP A 394 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 10.169A pdb=" N VAL A 370 " --> pdb=" O TRP A 394 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 413 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLU A 393 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR A 395 " --> pdb=" O TYR A 409 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N TYR A 409 " --> pdb=" O THR A 395 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG A 426 " --> pdb=" O GLN A 414 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 39 through 40 removed outlier: 6.375A pdb=" N VAL B 12 " --> pdb=" O TRP B 40 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N PHE B 13 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE B 69 " --> pdb=" O PHE B 13 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N SER B 15 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS B 135 " --> pdb=" O ILE B 102 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN B 104 " --> pdb=" O LYS B 135 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 188 through 191 removed outlier: 5.866A pdb=" N LEU B 168 " --> pdb=" O ARG B 229 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N GLU B 231 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU B 170 " --> pdb=" O GLU B 231 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 228 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL B 257 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ILE B 230 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 6.839A pdb=" N HIS B 329 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLU B 283 " --> pdb=" O TRP B 327 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TRP B 327 " --> pdb=" O GLU B 283 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ASP B 297 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP B 327 " --> pdb=" O ASP B 297 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA B 299 " --> pdb=" O TRP B 327 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N HIS B 329 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TYR B 301 " --> pdb=" O HIS B 329 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ALA B 331 " --> pdb=" O TYR B 301 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ASP B 303 " --> pdb=" O ALA B 331 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL B 298 " --> pdb=" O HIS B 367 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N MET B 369 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ALA B 300 " --> pdb=" O MET B 369 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ARG B 371 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE B 302 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 388 through 391 removed outlier: 3.634A pdb=" N VAL B 413 " --> pdb=" O ALA B 391 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG B 426 " --> pdb=" O GLN B 414 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ARG B 416 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ILE B 424 " --> pdb=" O ARG B 416 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.694A pdb=" N VAL C 12 " --> pdb=" O TRP C 40 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N PHE C 13 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE C 69 " --> pdb=" O PHE C 13 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N SER C 15 " --> pdb=" O ILE C 69 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 188 through 191 removed outlier: 3.600A pdb=" N GLU C 231 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU C 172 " --> pdb=" O GLU C 231 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL C 228 " --> pdb=" O THR C 255 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL C 257 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ILE C 230 " --> pdb=" O VAL C 257 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 278 through 283 removed outlier: 5.090A pdb=" N ILE C 280 " --> pdb=" O ALA C 331 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA C 331 " --> pdb=" O ILE C 280 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG C 282 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ASP C 297 " --> pdb=" O VAL C 325 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TRP C 327 " --> pdb=" O ASP C 297 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA C 299 " --> pdb=" O TRP C 327 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N HIS C 329 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TYR C 301 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ALA C 331 " --> pdb=" O TYR C 301 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL C 298 " --> pdb=" O HIS C 367 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N MET C 369 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA C 300 " --> pdb=" O MET C 369 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL C 370 " --> pdb=" O TYR C 392 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TRP C 394 " --> pdb=" O VAL C 370 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL C 413 " --> pdb=" O ALA C 391 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLU C 393 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N THR C 395 " --> pdb=" O TYR C 409 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N TYR C 409 " --> pdb=" O THR C 395 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG C 426 " --> pdb=" O GLN C 414 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ARG C 416 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ILE C 424 " --> pdb=" O ARG C 416 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 39 through 40 removed outlier: 5.929A pdb=" N VAL D 12 " --> pdb=" O TRP D 40 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE D 13 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ILE D 69 " --> pdb=" O PHE D 13 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N SER D 15 " --> pdb=" O ILE D 69 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 188 through 191 removed outlier: 5.995A pdb=" N LEU D 168 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N GLU D 231 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU D 170 " --> pdb=" O GLU D 231 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL D 228 " --> pdb=" O THR D 255 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL D 257 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE D 230 " --> pdb=" O VAL D 257 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 278 through 282 removed outlier: 5.716A pdb=" N ILE D 280 " --> pdb=" O ALA D 331 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ALA D 331 " --> pdb=" O ILE D 280 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL D 298 " --> pdb=" O HIS D 367 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N MET D 369 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA D 300 " --> pdb=" O MET D 369 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ARG D 371 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE D 302 " --> pdb=" O ARG D 371 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL D 366 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N TYR D 392 " --> pdb=" O VAL D 366 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU D 368 " --> pdb=" O TYR D 392 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N TRP D 394 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 10.414A pdb=" N VAL D 370 " --> pdb=" O TRP D 394 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL D 413 " --> pdb=" O ALA D 391 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU D 393 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR D 395 " --> pdb=" O TYR D 409 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N TYR D 409 " --> pdb=" O THR D 395 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLN D 414 " --> pdb=" O GLU D 425 " (cutoff:3.500A) 537 hydrogen bonds defined for protein. 1569 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: 2.17 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4615 1.34 - 1.46: 2149 1.46 - 1.58: 6908 1.58 - 1.70: 20 1.70 - 1.82: 64 Bond restraints: 13756 Sorted by residual: bond pdb=" N VAL B 389 " pdb=" CA VAL B 389 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.17e-02 7.31e+03 8.60e+00 bond pdb=" N HIS C 18 " pdb=" CA HIS C 18 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.57e+00 bond pdb=" N TYR C 16 " pdb=" CA TYR C 16 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.29e-02 6.01e+03 6.46e+00 bond pdb=" N TYR B 392 " pdb=" CA TYR B 392 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.39e-02 5.18e+03 6.40e+00 bond pdb=" N ARG B 388 " pdb=" CA ARG B 388 " ideal model delta sigma weight residual 1.456 1.487 -0.030 1.21e-02 6.83e+03 6.34e+00 ... (remaining 13751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 18477 2.51 - 5.03: 339 5.03 - 7.54: 36 7.54 - 10.05: 6 10.05 - 12.56: 2 Bond angle restraints: 18860 Sorted by residual: angle pdb=" N ARG B 416 " pdb=" CA ARG B 416 " pdb=" C ARG B 416 " ideal model delta sigma weight residual 107.70 120.26 -12.56 2.09e+00 2.29e-01 3.61e+01 angle pdb=" N VAL C 251 " pdb=" CA VAL C 251 " pdb=" C VAL C 251 " ideal model delta sigma weight residual 106.42 114.02 -7.60 1.51e+00 4.39e-01 2.53e+01 angle pdb=" N ASP B 396 " pdb=" CA ASP B 396 " pdb=" C ASP B 396 " ideal model delta sigma weight residual 112.41 106.58 5.83 1.30e+00 5.92e-01 2.01e+01 angle pdb=" C HIS A 197 " pdb=" N GLU A 198 " pdb=" CA GLU A 198 " ideal model delta sigma weight residual 121.54 129.54 -8.00 1.91e+00 2.74e-01 1.76e+01 angle pdb=" N VAL B 390 " pdb=" CA VAL B 390 " pdb=" C VAL B 390 " ideal model delta sigma weight residual 108.17 102.33 5.84 1.40e+00 5.10e-01 1.74e+01 ... (remaining 18855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.50: 7662 19.50 - 39.00: 574 39.00 - 58.50: 67 58.50 - 78.00: 20 78.00 - 97.50: 9 Dihedral angle restraints: 8332 sinusoidal: 3352 harmonic: 4980 Sorted by residual: dihedral pdb=" CA ILE D 37 " pdb=" C ILE D 37 " pdb=" N PRO D 38 " pdb=" CA PRO D 38 " ideal model delta harmonic sigma weight residual 180.00 152.30 27.70 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA VAL C 251 " pdb=" C VAL C 251 " pdb=" N GLY C 252 " pdb=" CA GLY C 252 " ideal model delta harmonic sigma weight residual 180.00 154.92 25.08 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA ASP C 45 " pdb=" C ASP C 45 " pdb=" N LEU C 46 " pdb=" CA LEU C 46 " ideal model delta harmonic sigma weight residual 180.00 155.85 24.15 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 8329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1802 0.059 - 0.118: 356 0.118 - 0.176: 37 0.176 - 0.235: 4 0.235 - 0.294: 1 Chirality restraints: 2200 Sorted by residual: chirality pdb=" CA VAL B 390 " pdb=" N VAL B 390 " pdb=" C VAL B 390 " pdb=" CB VAL B 390 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CB THR C 285 " pdb=" CA THR C 285 " pdb=" OG1 THR C 285 " pdb=" CG2 THR C 285 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CG LEU B 338 " pdb=" CB LEU B 338 " pdb=" CD1 LEU B 338 " pdb=" CD2 LEU B 338 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.97e-01 ... (remaining 2197 not shown) Planarity restraints: 2464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 246 " 0.058 5.00e-02 4.00e+02 8.71e-02 1.21e+01 pdb=" N PRO A 247 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO A 247 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 247 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 1 " 0.044 5.00e-02 4.00e+02 6.57e-02 6.91e+00 pdb=" N PRO D 2 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO D 2 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 2 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 409 " -0.019 2.00e-02 2.50e+03 1.82e-02 6.60e+00 pdb=" CG TYR A 409 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 409 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 409 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR A 409 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 409 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR A 409 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 409 " -0.006 2.00e-02 2.50e+03 ... (remaining 2461 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 361 2.67 - 3.23: 14162 3.23 - 3.79: 23185 3.79 - 4.34: 30228 4.34 - 4.90: 48193 Nonbonded interactions: 116129 Sorted by model distance: nonbonded pdb=" O MET C 254 " pdb=" OG SER C 266 " model vdw 2.117 3.040 nonbonded pdb=" OG1 THR D 395 " pdb=" O ARG D 408 " model vdw 2.119 3.040 nonbonded pdb=" OP2 A E 1 " pdb=" O2' A E 3 " model vdw 2.131 3.040 nonbonded pdb=" OH TYR D 16 " pdb=" OD1 ASP D 42 " model vdw 2.151 3.040 nonbonded pdb=" OG SER C 171 " pdb=" OD1 ASP C 189 " model vdw 2.169 3.040 ... (remaining 116124 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.610 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 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 : 0.004 0.040 13756 Z= 0.206 Angle : 0.814 12.563 18860 Z= 0.449 Chirality : 0.046 0.294 2200 Planarity : 0.006 0.087 2464 Dihedral : 13.773 97.499 5108 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 25.90 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.22 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.20), residues: 1724 helix: 1.41 (0.22), residues: 560 sheet: 0.28 (0.29), residues: 328 loop : -1.25 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 382 TYR 0.039 0.003 TYR A 409 PHE 0.016 0.002 PHE C 215 TRP 0.040 0.003 TRP A 327 HIS 0.010 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00413 (13756) covalent geometry : angle 0.81446 (18860) hydrogen bonds : bond 0.17368 ( 537) hydrogen bonds : angle 7.10527 ( 1569) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 359 MET cc_start: 0.3587 (tmm) cc_final: 0.2955 (tpt) REVERT: A 368 LEU cc_start: 0.8443 (tp) cc_final: 0.8221 (tt) REVERT: B 17 ARG cc_start: 0.6035 (mmt180) cc_final: 0.5630 (mmt180) REVERT: B 31 LEU cc_start: 0.8650 (mm) cc_final: 0.8312 (mm) REVERT: B 42 ASP cc_start: 0.7820 (m-30) cc_final: 0.7330 (t0) REVERT: B 145 MET cc_start: 0.8147 (tmm) cc_final: 0.7431 (tmm) REVERT: B 187 ASP cc_start: 0.7106 (m-30) cc_final: 0.6869 (m-30) REVERT: C 357 LEU cc_start: 0.7954 (tp) cc_final: 0.7245 (tp) REVERT: D 207 GLU cc_start: 0.8490 (tp30) cc_final: 0.8272 (tt0) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.1051 time to fit residues: 43.0291 Evaluate side-chains 192 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN A 263 HIS A 305 GLN A 315 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 GLN ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 ASN C 363 ASN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.124510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.109497 restraints weight = 26902.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.112607 restraints weight = 13888.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.114742 restraints weight = 8538.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.116153 restraints weight = 5917.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.116945 restraints weight = 4536.077| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13756 Z= 0.179 Angle : 0.731 9.177 18860 Z= 0.361 Chirality : 0.047 0.168 2200 Planarity : 0.006 0.056 2464 Dihedral : 8.473 98.613 2048 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 20.82 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.45 % Favored : 94.37 % Rotamer: Outliers : 1.51 % Allowed : 10.92 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.20), residues: 1724 helix: 1.26 (0.21), residues: 572 sheet: -0.01 (0.30), residues: 328 loop : -1.32 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 355 TYR 0.022 0.002 TYR D 16 PHE 0.016 0.002 PHE B 404 TRP 0.026 0.002 TRP A 394 HIS 0.011 0.001 HIS D 152 Details of bonding type rmsd covalent geometry : bond 0.00410 (13756) covalent geometry : angle 0.73084 (18860) hydrogen bonds : bond 0.05080 ( 537) hydrogen bonds : angle 6.00502 ( 1569) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 233 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.8254 (tpp-160) cc_final: 0.7955 (tpp-160) REVERT: A 359 MET cc_start: 0.3819 (tmm) cc_final: 0.3176 (tpt) REVERT: A 393 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7162 (mm-30) REVERT: B 104 ASN cc_start: 0.7969 (t0) cc_final: 0.7667 (t0) REVERT: B 145 MET cc_start: 0.8370 (tmm) cc_final: 0.7942 (tmm) REVERT: B 187 ASP cc_start: 0.7484 (m-30) cc_final: 0.7183 (m-30) REVERT: B 369 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.7077 (ttm) REVERT: C 84 GLU cc_start: 0.7048 (tt0) cc_final: 0.6564 (tt0) REVERT: C 135 LYS cc_start: 0.7842 (mmmt) cc_final: 0.7642 (mmtt) REVERT: C 149 MET cc_start: 0.8116 (tpp) cc_final: 0.7628 (tpp) REVERT: C 361 ASN cc_start: 0.7815 (m-40) cc_final: 0.7482 (m110) REVERT: D 145 MET cc_start: 0.8127 (tmm) cc_final: 0.7789 (tpp) REVERT: D 149 MET cc_start: 0.7535 (tpp) cc_final: 0.7011 (mpp) REVERT: D 242 ILE cc_start: 0.8632 (tp) cc_final: 0.8381 (tt) outliers start: 21 outliers final: 11 residues processed: 246 average time/residue: 0.1149 time to fit residues: 41.7961 Evaluate side-chains 203 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 191 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 398 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 165 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 164 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 chunk 140 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 143 optimal weight: 9.9990 chunk 90 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN A 176 ASN A 179 GLN A 315 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 GLN C 385 ASN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.125314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.110303 restraints weight = 27209.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.113485 restraints weight = 13946.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.115605 restraints weight = 8512.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.117037 restraints weight = 5900.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.117965 restraints weight = 4487.694| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13756 Z= 0.148 Angle : 0.682 8.983 18860 Z= 0.336 Chirality : 0.046 0.162 2200 Planarity : 0.006 0.049 2464 Dihedral : 8.345 94.264 2048 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.28 % Favored : 94.55 % Rotamer: Outliers : 1.72 % Allowed : 14.94 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.20), residues: 1724 helix: 1.33 (0.21), residues: 572 sheet: -0.49 (0.28), residues: 352 loop : -1.25 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 147 TYR 0.021 0.002 TYR D 16 PHE 0.014 0.002 PHE C 404 TRP 0.014 0.002 TRP A 394 HIS 0.010 0.001 HIS D 152 Details of bonding type rmsd covalent geometry : bond 0.00347 (13756) covalent geometry : angle 0.68245 (18860) hydrogen bonds : bond 0.04262 ( 537) hydrogen bonds : angle 5.80578 ( 1569) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 242 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.4905 (p90) cc_final: 0.4690 (p90) REVERT: A 359 MET cc_start: 0.3511 (tmm) cc_final: 0.2913 (tpt) REVERT: A 383 LEU cc_start: 0.9058 (mt) cc_final: 0.8848 (mp) REVERT: B 104 ASN cc_start: 0.8120 (t0) cc_final: 0.7753 (t0) REVERT: B 145 MET cc_start: 0.8546 (tmm) cc_final: 0.8091 (tmm) REVERT: B 187 ASP cc_start: 0.7504 (m-30) cc_final: 0.7230 (m-30) REVERT: C 84 GLU cc_start: 0.6981 (tt0) cc_final: 0.6475 (tt0) REVERT: C 149 MET cc_start: 0.8198 (tpp) cc_final: 0.7703 (tpp) REVERT: C 264 TRP cc_start: 0.8531 (m100) cc_final: 0.8314 (m100) REVERT: D 145 MET cc_start: 0.8033 (tmm) cc_final: 0.7733 (tpp) REVERT: D 149 MET cc_start: 0.7563 (tpp) cc_final: 0.6983 (tpp) REVERT: D 174 THR cc_start: 0.8605 (p) cc_final: 0.8399 (t) REVERT: D 242 ILE cc_start: 0.8611 (tp) cc_final: 0.8408 (tt) outliers start: 24 outliers final: 10 residues processed: 258 average time/residue: 0.1172 time to fit residues: 44.6328 Evaluate side-chains 202 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 192 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 398 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 58 optimal weight: 0.6980 chunk 152 optimal weight: 10.0000 chunk 169 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN A 176 ASN A 306 HIS A 315 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 ASN C 363 ASN C 367 HIS D 104 ASN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.121978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.107185 restraints weight = 27435.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.110238 restraints weight = 14382.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.112310 restraints weight = 8897.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.113730 restraints weight = 6203.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.114671 restraints weight = 4721.013| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13756 Z= 0.186 Angle : 0.700 9.173 18860 Z= 0.345 Chirality : 0.045 0.182 2200 Planarity : 0.006 0.049 2464 Dihedral : 8.377 94.686 2048 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.39 % Favored : 94.43 % Rotamer: Outliers : 3.23 % Allowed : 15.66 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.20), residues: 1724 helix: 1.32 (0.22), residues: 572 sheet: -0.67 (0.28), residues: 352 loop : -1.27 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 175 TYR 0.018 0.002 TYR D 16 PHE 0.032 0.002 PHE D 98 TRP 0.020 0.002 TRP D 327 HIS 0.010 0.001 HIS D 152 Details of bonding type rmsd covalent geometry : bond 0.00436 (13756) covalent geometry : angle 0.69973 (18860) hydrogen bonds : bond 0.04149 ( 537) hydrogen bonds : angle 5.71326 ( 1569) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 203 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 MET cc_start: 0.3594 (tmm) cc_final: 0.2875 (tpt) REVERT: A 383 LEU cc_start: 0.9079 (mt) cc_final: 0.8864 (mp) REVERT: B 104 ASN cc_start: 0.8158 (t0) cc_final: 0.7870 (t0) REVERT: B 187 ASP cc_start: 0.7597 (m-30) cc_final: 0.7300 (m-30) REVERT: C 84 GLU cc_start: 0.6942 (tt0) cc_final: 0.6435 (tt0) REVERT: C 145 MET cc_start: 0.9058 (tmm) cc_final: 0.8198 (tmm) REVERT: C 149 MET cc_start: 0.8143 (tpp) cc_final: 0.7735 (tpp) REVERT: C 264 TRP cc_start: 0.8553 (m100) cc_final: 0.8351 (m100) REVERT: C 269 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7023 (mm-30) REVERT: C 404 PHE cc_start: 0.7739 (t80) cc_final: 0.7424 (t80) REVERT: D 145 MET cc_start: 0.7934 (tmm) cc_final: 0.7701 (tpp) REVERT: D 149 MET cc_start: 0.7705 (tpp) cc_final: 0.7174 (tpp) REVERT: D 174 THR cc_start: 0.8348 (p) cc_final: 0.8096 (t) outliers start: 45 outliers final: 23 residues processed: 235 average time/residue: 0.1023 time to fit residues: 36.5367 Evaluate side-chains 206 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 398 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 78 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 161 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN A 315 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 HIS C 363 ASN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.114239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.099435 restraints weight = 28063.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.102311 restraints weight = 14942.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.104266 restraints weight = 9416.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.105582 restraints weight = 6671.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.106529 restraints weight = 5181.484| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 13756 Z= 0.294 Angle : 0.785 10.106 18860 Z= 0.393 Chirality : 0.048 0.208 2200 Planarity : 0.007 0.073 2464 Dihedral : 8.599 95.477 2048 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 24.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.03 % Favored : 93.85 % Rotamer: Outliers : 3.88 % Allowed : 17.31 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.20), residues: 1724 helix: 1.02 (0.21), residues: 572 sheet: -0.99 (0.28), residues: 348 loop : -1.33 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 382 TYR 0.021 0.003 TYR D 16 PHE 0.028 0.003 PHE D 98 TRP 0.024 0.003 TRP C 394 HIS 0.011 0.002 HIS D 152 Details of bonding type rmsd covalent geometry : bond 0.00671 (13756) covalent geometry : angle 0.78501 (18860) hydrogen bonds : bond 0.04613 ( 537) hydrogen bonds : angle 5.84010 ( 1569) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 193 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 MET cc_start: 0.7247 (tpp) cc_final: 0.6917 (tpp) REVERT: A 410 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6094 (mp0) REVERT: B 104 ASN cc_start: 0.8316 (t0) cc_final: 0.8006 (t0) REVERT: B 187 ASP cc_start: 0.7918 (m-30) cc_final: 0.7701 (m-30) REVERT: B 369 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7759 (ttm) REVERT: C 145 MET cc_start: 0.9021 (tmm) cc_final: 0.8454 (tmm) REVERT: C 198 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7953 (pm20) REVERT: C 212 THR cc_start: 0.8799 (p) cc_final: 0.8592 (p) REVERT: C 269 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7126 (mm-30) REVERT: C 404 PHE cc_start: 0.7930 (t80) cc_final: 0.7547 (t80) REVERT: D 174 THR cc_start: 0.8541 (p) cc_final: 0.8319 (t) REVERT: D 369 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7588 (tpp) outliers start: 54 outliers final: 33 residues processed: 230 average time/residue: 0.0937 time to fit residues: 34.0370 Evaluate side-chains 215 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 178 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 369 MET Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 398 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 145 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 131 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.119466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.104586 restraints weight = 27278.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.107685 restraints weight = 14028.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.109785 restraints weight = 8612.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.111166 restraints weight = 5976.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.112167 restraints weight = 4566.072| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13756 Z= 0.157 Angle : 0.701 10.734 18860 Z= 0.345 Chirality : 0.046 0.251 2200 Planarity : 0.006 0.061 2464 Dihedral : 8.459 98.251 2048 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.34 % Favored : 94.61 % Rotamer: Outliers : 3.38 % Allowed : 18.39 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.20), residues: 1724 helix: 1.21 (0.22), residues: 572 sheet: -0.89 (0.29), residues: 340 loop : -1.21 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 382 TYR 0.022 0.002 TYR D 16 PHE 0.022 0.002 PHE D 98 TRP 0.024 0.002 TRP C 394 HIS 0.010 0.001 HIS D 152 Details of bonding type rmsd covalent geometry : bond 0.00371 (13756) covalent geometry : angle 0.70135 (18860) hydrogen bonds : bond 0.04042 ( 537) hydrogen bonds : angle 5.67392 ( 1569) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 214 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.4825 (p90) cc_final: 0.4610 (p90) REVERT: A 17 ARG cc_start: 0.6783 (mmp80) cc_final: 0.6397 (mmp80) REVERT: A 424 ILE cc_start: 0.9209 (mm) cc_final: 0.9000 (mt) REVERT: B 16 TYR cc_start: 0.7285 (p90) cc_final: 0.6802 (p90) REVERT: B 104 ASN cc_start: 0.8267 (t0) cc_final: 0.8033 (t0) REVERT: B 187 ASP cc_start: 0.7727 (m-30) cc_final: 0.7445 (m-30) REVERT: B 202 SER cc_start: 0.8237 (t) cc_final: 0.8019 (m) REVERT: C 84 GLU cc_start: 0.6897 (tt0) cc_final: 0.6625 (tt0) REVERT: C 269 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7110 (mm-30) REVERT: C 371 ARG cc_start: 0.8266 (mtp-110) cc_final: 0.7881 (ttt90) REVERT: C 394 TRP cc_start: 0.5309 (p-90) cc_final: 0.5061 (p-90) REVERT: C 404 PHE cc_start: 0.7829 (t80) cc_final: 0.7553 (t80) REVERT: D 174 THR cc_start: 0.8477 (p) cc_final: 0.8211 (t) REVERT: D 424 ILE cc_start: 0.9417 (OUTLIER) cc_final: 0.9135 (mm) outliers start: 47 outliers final: 29 residues processed: 248 average time/residue: 0.1100 time to fit residues: 41.2131 Evaluate side-chains 230 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 424 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 158 optimal weight: 0.0040 chunk 116 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 138 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 ASN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 ASN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.121037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.106275 restraints weight = 27436.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.109417 restraints weight = 13918.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.111518 restraints weight = 8431.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.112929 restraints weight = 5802.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.113880 restraints weight = 4386.385| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13756 Z= 0.147 Angle : 0.709 10.949 18860 Z= 0.345 Chirality : 0.046 0.363 2200 Planarity : 0.006 0.050 2464 Dihedral : 8.363 96.791 2048 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.86 % Favored : 94.08 % Rotamer: Outliers : 3.30 % Allowed : 19.68 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.20), residues: 1724 helix: 1.27 (0.21), residues: 572 sheet: -0.98 (0.29), residues: 340 loop : -1.16 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 147 TYR 0.026 0.002 TYR D 16 PHE 0.023 0.002 PHE B 215 TRP 0.031 0.002 TRP A 394 HIS 0.015 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00352 (13756) covalent geometry : angle 0.70924 (18860) hydrogen bonds : bond 0.03899 ( 537) hydrogen bonds : angle 5.60729 ( 1569) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 215 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 ASN cc_start: 0.7448 (OUTLIER) cc_final: 0.7226 (p0) REVERT: A 10 ASP cc_start: 0.7525 (m-30) cc_final: 0.7258 (m-30) REVERT: A 16 TYR cc_start: 0.5009 (p90) cc_final: 0.4752 (p90) REVERT: A 17 ARG cc_start: 0.6787 (mmp80) cc_final: 0.6473 (mmp80) REVERT: B 104 ASN cc_start: 0.8206 (t0) cc_final: 0.7994 (t0) REVERT: B 187 ASP cc_start: 0.7538 (m-30) cc_final: 0.7284 (m-30) REVERT: B 202 SER cc_start: 0.8256 (t) cc_final: 0.8050 (m) REVERT: C 84 GLU cc_start: 0.6916 (tt0) cc_final: 0.6621 (tt0) REVERT: C 120 ARG cc_start: 0.8584 (tmm-80) cc_final: 0.8341 (ptt90) REVERT: C 269 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7331 (mm-30) REVERT: C 404 PHE cc_start: 0.7822 (t80) cc_final: 0.7561 (t80) REVERT: D 145 MET cc_start: 0.8283 (tmm) cc_final: 0.7551 (tpp) REVERT: D 174 THR cc_start: 0.8473 (p) cc_final: 0.8190 (t) REVERT: D 424 ILE cc_start: 0.9403 (OUTLIER) cc_final: 0.9098 (mm) outliers start: 46 outliers final: 33 residues processed: 247 average time/residue: 0.1017 time to fit residues: 38.4210 Evaluate side-chains 232 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 424 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 29 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 156 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 ASN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.121758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.107010 restraints weight = 27209.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.110181 restraints weight = 13795.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.112240 restraints weight = 8324.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.113623 restraints weight = 5741.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.114540 restraints weight = 4365.415| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13756 Z= 0.155 Angle : 0.716 10.890 18860 Z= 0.349 Chirality : 0.047 0.328 2200 Planarity : 0.006 0.047 2464 Dihedral : 8.293 95.185 2048 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.74 % Favored : 94.20 % Rotamer: Outliers : 3.38 % Allowed : 20.98 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.20), residues: 1724 helix: 1.30 (0.22), residues: 572 sheet: -1.05 (0.28), residues: 340 loop : -1.16 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 126 TYR 0.029 0.002 TYR D 301 PHE 0.020 0.002 PHE A 215 TRP 0.030 0.002 TRP A 394 HIS 0.012 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00377 (13756) covalent geometry : angle 0.71561 (18860) hydrogen bonds : bond 0.03899 ( 537) hydrogen bonds : angle 5.58417 ( 1569) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 215 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7565 (mtp) REVERT: A 355 ARG cc_start: 0.7139 (mtp180) cc_final: 0.4338 (tmt170) REVERT: B 40 TRP cc_start: 0.8515 (t60) cc_final: 0.8269 (t60) REVERT: B 202 SER cc_start: 0.8235 (t) cc_final: 0.7998 (m) REVERT: C 84 GLU cc_start: 0.6756 (tt0) cc_final: 0.6367 (tt0) REVERT: C 120 ARG cc_start: 0.8551 (tmm-80) cc_final: 0.8290 (ptt90) REVERT: C 254 MET cc_start: 0.7706 (ttm) cc_final: 0.7496 (ttp) REVERT: C 269 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7311 (mm-30) REVERT: C 404 PHE cc_start: 0.7874 (t80) cc_final: 0.7640 (t80) REVERT: D 174 THR cc_start: 0.8456 (p) cc_final: 0.8181 (t) REVERT: D 424 ILE cc_start: 0.9391 (OUTLIER) cc_final: 0.9090 (mm) outliers start: 47 outliers final: 35 residues processed: 246 average time/residue: 0.1058 time to fit residues: 39.5964 Evaluate side-chains 237 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 200 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 424 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 2 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 132 optimal weight: 0.5980 chunk 71 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 164 optimal weight: 6.9990 chunk 116 optimal weight: 0.1980 chunk 69 optimal weight: 6.9990 chunk 93 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 ASN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.124473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.110496 restraints weight = 26925.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.113614 restraints weight = 13454.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.115662 restraints weight = 7997.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.117042 restraints weight = 5401.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.117936 restraints weight = 4037.844| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13756 Z= 0.140 Angle : 0.717 11.088 18860 Z= 0.347 Chirality : 0.046 0.349 2200 Planarity : 0.006 0.052 2464 Dihedral : 8.177 93.915 2048 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.45 % Favored : 94.49 % Rotamer: Outliers : 2.95 % Allowed : 21.84 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.20), residues: 1724 helix: 1.38 (0.22), residues: 572 sheet: -1.11 (0.28), residues: 340 loop : -1.12 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 371 TYR 0.022 0.003 TYR D 301 PHE 0.025 0.002 PHE B 215 TRP 0.069 0.003 TRP D 394 HIS 0.010 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00335 (13756) covalent geometry : angle 0.71729 (18860) hydrogen bonds : bond 0.03725 ( 537) hydrogen bonds : angle 5.56602 ( 1569) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 219 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.6499 (mmp80) cc_final: 0.6282 (mmp80) REVERT: A 149 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7415 (mtp) REVERT: A 355 ARG cc_start: 0.6968 (mtp180) cc_final: 0.4221 (tmt170) REVERT: A 369 MET cc_start: 0.7589 (tpp) cc_final: 0.7171 (tpp) REVERT: B 100 LEU cc_start: 0.8486 (tp) cc_final: 0.8279 (mt) REVERT: B 145 MET cc_start: 0.8650 (tpp) cc_final: 0.8010 (tpp) REVERT: B 202 SER cc_start: 0.8178 (t) cc_final: 0.7969 (m) REVERT: C 84 GLU cc_start: 0.6744 (tt0) cc_final: 0.6348 (tt0) REVERT: C 177 THR cc_start: 0.8594 (m) cc_final: 0.8307 (m) REVERT: C 269 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7291 (mm-30) REVERT: C 371 ARG cc_start: 0.7400 (ttt90) cc_final: 0.7139 (mtp-110) REVERT: D 174 THR cc_start: 0.8447 (p) cc_final: 0.8134 (t) REVERT: D 424 ILE cc_start: 0.9365 (OUTLIER) cc_final: 0.9054 (mm) outliers start: 41 outliers final: 34 residues processed: 245 average time/residue: 0.1134 time to fit residues: 41.1113 Evaluate side-chains 236 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 424 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 47 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 120 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 ASN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 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 = 0.3801 r_free = 0.3801 target = 0.125080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.110520 restraints weight = 27264.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.113615 restraints weight = 13917.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.115684 restraints weight = 8448.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.116994 restraints weight = 5822.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.117993 restraints weight = 4450.318| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13756 Z= 0.147 Angle : 0.725 11.619 18860 Z= 0.351 Chirality : 0.046 0.326 2200 Planarity : 0.006 0.049 2464 Dihedral : 8.134 95.021 2048 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 20.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.63 % Favored : 94.32 % Rotamer: Outliers : 2.59 % Allowed : 22.34 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.20), residues: 1724 helix: 1.36 (0.21), residues: 572 sheet: -1.15 (0.27), residues: 340 loop : -1.11 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 126 TYR 0.019 0.002 TYR B 16 PHE 0.023 0.003 PHE A 215 TRP 0.042 0.003 TRP A 394 HIS 0.006 0.001 HIS D 152 Details of bonding type rmsd covalent geometry : bond 0.00354 (13756) covalent geometry : angle 0.72460 (18860) hydrogen bonds : bond 0.03707 ( 537) hydrogen bonds : angle 5.57840 ( 1569) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.6894 (mtp180) cc_final: 0.4166 (tmt170) REVERT: B 100 LEU cc_start: 0.8518 (tp) cc_final: 0.8312 (mt) REVERT: B 145 MET cc_start: 0.8560 (tpp) cc_final: 0.7895 (tpp) REVERT: B 229 ARG cc_start: 0.7969 (ttt180) cc_final: 0.7528 (ttt180) REVERT: C 84 GLU cc_start: 0.6698 (tt0) cc_final: 0.6349 (tt0) REVERT: C 177 THR cc_start: 0.8569 (m) cc_final: 0.8272 (m) REVERT: C 269 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7246 (mm-30) REVERT: C 371 ARG cc_start: 0.7418 (ttt90) cc_final: 0.7185 (mtp-110) REVERT: D 424 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9041 (mm) outliers start: 36 outliers final: 30 residues processed: 229 average time/residue: 0.0929 time to fit residues: 33.3240 Evaluate side-chains 228 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 197 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 424 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 150 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 171 optimal weight: 0.0270 chunk 148 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 overall best weight: 1.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 HIS ** 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 = 0.3749 r_free = 0.3749 target = 0.121340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.106252 restraints weight = 27691.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.109349 restraints weight = 14185.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.111425 restraints weight = 8672.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.112811 restraints weight = 6018.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.113712 restraints weight = 4591.702| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13756 Z= 0.181 Angle : 0.736 11.857 18860 Z= 0.357 Chirality : 0.046 0.352 2200 Planarity : 0.006 0.049 2464 Dihedral : 8.143 96.535 2048 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 21.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.51 % Allowed : 22.56 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.20), residues: 1724 helix: 1.33 (0.22), residues: 572 sheet: -1.24 (0.27), residues: 340 loop : -1.13 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 371 TYR 0.022 0.003 TYR B 16 PHE 0.022 0.003 PHE C 404 TRP 0.062 0.003 TRP C 394 HIS 0.007 0.001 HIS D 152 Details of bonding type rmsd covalent geometry : bond 0.00429 (13756) covalent geometry : angle 0.73582 (18860) hydrogen bonds : bond 0.03815 ( 537) hydrogen bonds : angle 5.58283 ( 1569) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2055.62 seconds wall clock time: 36 minutes 27.92 seconds (2187.92 seconds total)