Starting phenix.real_space_refine on Sat Sep 12 03:35:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7qqk_14122/09_2026/7qqk_14122.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qqk_14122/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7qqk_14122/09_2026/7qqk_14122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qqk_14122/09_2026/7qqk_14122.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7qqk_14122/09_2026/7qqk_14122.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7qqk_14122/09_2026/7qqk_14122.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qqk_14122/09_2026/7qqk_14122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qqk_14122/09_2026/7qqk_14122.map" } 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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 3} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Time building chain proxies: 2.74, per 1000 atoms: 0.20 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: 0.89 Conformation dependent library (CDL) restraints added in 524.8 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: 0.39 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: 2.65 Time building geometry restraints manager: 1.17 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: 18430 2.51 - 5.03: 385 5.03 - 7.54: 37 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 - 17.81: 7504 17.81 - 35.61: 661 35.61 - 53.42: 103 53.42 - 71.23: 48 71.23 - 89.03: 16 Dihedral angle restraints: 8332 sinusoidal: 3352 harmonic: 4980 Sorted by residual: dihedral pdb=" C4' A H 2 " pdb=" C3' A H 2 " pdb=" C2' A H 2 " pdb=" C1' A H 2 " ideal model delta sinusoidal sigma weight residual 36.34 -36.39 72.73 1 3.10e+00 1.04e-01 7.02e+02 dihedral pdb=" C4' A F 3 " pdb=" C3' A F 3 " pdb=" C2' A F 3 " pdb=" C1' A F 3 " ideal model delta sinusoidal sigma weight residual 36.34 -35.72 72.06 1 3.10e+00 1.04e-01 6.91e+02 dihedral pdb=" C4' A E 3 " pdb=" C3' A E 3 " pdb=" C2' A E 3 " pdb=" C1' A E 3 " ideal model delta sinusoidal sigma weight residual 36.35 -35.70 72.04 1 3.10e+00 1.04e-01 6.91e+02 ... (remaining 8329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1776 0.059 - 0.118: 354 0.118 - 0.176: 37 0.176 - 0.235: 12 0.235 - 0.294: 21 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=" C2' A H 2 " pdb=" C3' A H 2 " pdb=" O2' A H 2 " pdb=" C1' A H 2 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C2' A G 2 " pdb=" C3' A G 2 " pdb=" O2' A G 2 " pdb=" C1' A G 2 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.95e+00 ... (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: 6.170 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.710 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 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= 0.207 Angle : 0.840 12.563 18860 Z= 0.459 Chirality : 0.054 0.294 2200 Planarity : 0.006 0.087 2464 Dihedral : 14.602 89.033 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/Z covalent geometry : bond 0.00417 / 0.21 (13756) covalent geometry : angle 0.83961 / 0.46 (18860) hydrogen bonds : bond 0.17368 / 11.64 ( 537) hydrogen bonds : angle 7.10527 / 5.12 ( 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 : 0.532 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: 0.1029 time to fit residues: 42.2942 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 : 0.469 ------------------------------------------------------------------------------- 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... 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 ** 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 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 Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.124842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.109759 restraints weight = 26871.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.112909 restraints weight = 13935.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.115069 restraints weight = 8556.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.116538 restraints weight = 5909.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.117493 restraints weight = 4477.734| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13756 Z= 0.190 Angle : 0.811 10.813 18860 Z= 0.394 Chirality : 0.055 0.815 2200 Planarity : 0.006 0.057 2464 Dihedral : 8.689 139.190 2048 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 21.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.34 % Favored : 94.49 % Rotamer: Outliers : 1.44 % Allowed : 10.78 % Favored : 87.79 % 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: -0.29 (0.20), residues: 1724 helix: 1.25 (0.21), residues: 572 sheet: -0.07 (0.29), residues: 332 loop : -1.30 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 408 TYR 0.023 0.002 TYR D 16 PHE 0.018 0.002 PHE A 404 TRP 0.030 0.003 TRP C 394 HIS 0.011 0.002 HIS D 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (13756) covalent geometry : angle 0.81074 / 0.39 (18860) hydrogen bonds : bond 0.05074 / 3.42 ( 537) hydrogen bonds : angle 6.05246 / 4.41 ( 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: 20 poor density : 234 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.8258 (tpp-160) cc_final: 0.7882 (tpp-160) REVERT: A 359 MET cc_start: 0.3811 (tmm) cc_final: 0.3162 (tpt) REVERT: B 104 ASN cc_start: 0.7973 (t0) cc_final: 0.7672 (t0) REVERT: B 145 MET cc_start: 0.8360 (tmm) cc_final: 0.7933 (tmm) REVERT: B 187 ASP cc_start: 0.7449 (m-30) cc_final: 0.7149 (m-30) REVERT: B 369 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.7022 (ttm) REVERT: C 84 GLU cc_start: 0.7023 (tt0) cc_final: 0.6540 (tt0) REVERT: C 135 LYS cc_start: 0.7854 (mmmt) cc_final: 0.7649 (mmtt) REVERT: C 149 MET cc_start: 0.8100 (tpp) cc_final: 0.7608 (tpp) REVERT: C 361 ASN cc_start: 0.7819 (m-40) cc_final: 0.7481 (m110) REVERT: C 404 PHE cc_start: 0.7745 (t80) cc_final: 0.7243 (t80) REVERT: D 242 ILE cc_start: 0.8648 (tp) cc_final: 0.8373 (tt) outliers start: 20 outliers final: 11 residues processed: 248 average time/residue: 0.1034 time to fit residues: 38.5619 Evaluate side-chains 197 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 185 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 239 SER Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 380 ILE 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: 0.7980 chunk 50 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 164 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 ASN A 315 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 ASN 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.125161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.110125 restraints weight = 27209.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.113295 restraints weight = 14037.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.115433 restraints weight = 8597.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.116866 restraints weight = 5945.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.117872 restraints weight = 4519.789| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1806 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= 0.158 Angle : 0.736 8.814 18860 Z= 0.358 Chirality : 0.051 0.506 2200 Planarity : 0.006 0.049 2464 Dihedral : 8.616 165.541 2048 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.28 % Favored : 94.55 % Rotamer: Outliers : 1.80 % Allowed : 13.86 % Favored : 84.34 % 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: 1.31 (0.21), residues: 572 sheet: -0.46 (0.28), residues: 352 loop : -1.25 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 277 TYR 0.020 0.002 TYR D 16 PHE 0.012 0.002 PHE B 209 TRP 0.017 0.002 TRP C 394 HIS 0.010 0.001 HIS D 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (13756) covalent geometry : angle 0.73569 / 0.36 (18860) hydrogen bonds : bond 0.04346 / 2.93 ( 537) hydrogen bonds : angle 5.84379 / 4.26 ( 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 265 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 240 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.4841 (p90) cc_final: 0.4637 (p90) REVERT: A 359 MET cc_start: 0.3500 (tmm) cc_final: 0.2893 (tpt) REVERT: A 383 LEU cc_start: 0.9069 (mt) cc_final: 0.8839 (mp) REVERT: B 42 ASP cc_start: 0.7737 (m-30) cc_final: 0.7220 (t0) REVERT: B 104 ASN cc_start: 0.8090 (t0) cc_final: 0.7698 (t0) REVERT: B 145 MET cc_start: 0.8500 (tmm) cc_final: 0.8079 (tmm) REVERT: B 187 ASP cc_start: 0.7468 (m-30) cc_final: 0.7219 (m-30) REVERT: C 84 GLU cc_start: 0.7012 (tt0) cc_final: 0.6497 (tt0) REVERT: C 149 MET cc_start: 0.8193 (tpp) cc_final: 0.7703 (tpp) REVERT: C 264 TRP cc_start: 0.8530 (m100) cc_final: 0.8317 (m100) REVERT: C 371 ARG cc_start: 0.8304 (mtp-110) cc_final: 0.7933 (ttt90) REVERT: C 394 TRP cc_start: 0.4284 (p-90) cc_final: 0.3870 (p-90) REVERT: C 404 PHE cc_start: 0.7716 (t80) cc_final: 0.7376 (t80) REVERT: D 149 MET cc_start: 0.7502 (tpp) cc_final: 0.7282 (mpp) REVERT: D 174 THR cc_start: 0.8636 (p) cc_final: 0.8369 (t) outliers start: 25 outliers final: 13 residues processed: 254 average time/residue: 0.1064 time to fit residues: 40.4543 Evaluate side-chains 211 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 198 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 C residue 363 ASN Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 351 VAL 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: 8.9990 chunk 152 optimal weight: 0.9990 chunk 169 optimal weight: 8.9990 chunk 115 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 GLN A 176 ASN ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 GLN C 305 GLN C 361 ASN C 363 ASN D 104 ASN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.119015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.104019 restraints weight = 27592.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.107097 restraints weight = 14243.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.109118 restraints weight = 8740.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.110499 restraints weight = 6132.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.111451 restraints weight = 4703.645| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13756 Z= 0.226 Angle : 0.754 8.877 18860 Z= 0.371 Chirality : 0.051 0.318 2200 Planarity : 0.006 0.065 2464 Dihedral : 8.690 169.411 2048 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 23.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.80 % Favored : 94.03 % Rotamer: Outliers : 3.23 % Allowed : 16.31 % Favored : 80.46 % 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: -0.54 (0.20), residues: 1724 helix: 1.15 (0.21), residues: 572 sheet: -0.73 (0.28), residues: 344 loop : -1.29 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 277 TYR 0.020 0.003 TYR D 16 PHE 0.031 0.002 PHE D 98 TRP 0.020 0.002 TRP C 394 HIS 0.010 0.002 HIS D 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.23 (13756) covalent geometry : angle 0.75424 / 0.37 (18860) hydrogen bonds : bond 0.04391 / 2.96 ( 537) hydrogen bonds : angle 5.81127 / 4.23 ( 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 250 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 MET cc_start: 0.3637 (tmm) cc_final: 0.2905 (tpt) REVERT: A 410 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6447 (mp0) REVERT: B 42 ASP cc_start: 0.7774 (m-30) cc_final: 0.7320 (t0) REVERT: B 104 ASN cc_start: 0.8219 (t0) cc_final: 0.7894 (t0) REVERT: B 187 ASP cc_start: 0.7766 (m-30) cc_final: 0.7456 (m-30) REVERT: C 84 GLU cc_start: 0.6991 (tt0) cc_final: 0.6456 (tt0) REVERT: C 145 MET cc_start: 0.9098 (tmm) cc_final: 0.8256 (tmm) REVERT: C 149 MET cc_start: 0.8272 (tpp) cc_final: 0.7812 (tpp) REVERT: C 269 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7105 (mm-30) REVERT: C 404 PHE cc_start: 0.7827 (t80) cc_final: 0.7557 (t80) REVERT: D 174 THR cc_start: 0.8442 (p) cc_final: 0.8154 (t) outliers start: 45 outliers final: 24 residues processed: 233 average time/residue: 0.0976 time to fit residues: 34.9266 Evaluate side-chains 212 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 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 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 268 THR Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 365 VAL 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: 0.8980 chunk 123 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 110 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 ASN ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** B 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 GLN C 361 ASN ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3719 r_free = 0.3719 target = 0.119296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.104377 restraints weight = 27398.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.107460 restraints weight = 14120.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.109531 restraints weight = 8653.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.110886 restraints weight = 6012.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.111829 restraints weight = 4615.542| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13756 Z= 0.192 Angle : 0.734 10.251 18860 Z= 0.358 Chirality : 0.050 0.325 2200 Planarity : 0.006 0.051 2464 Dihedral : 8.636 172.355 2048 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 22.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.57 % Favored : 94.32 % Rotamer: Outliers : 3.74 % Allowed : 17.67 % Favored : 78.59 % 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 (0.21), residues: 572 sheet: -0.78 (0.29), residues: 344 loop : -1.28 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 126 TYR 0.024 0.002 TYR D 301 PHE 0.027 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/Z covalent geometry : bond 0.00451 / 0.19 (13756) covalent geometry : angle 0.73368 / 0.36 (18860) hydrogen bonds : bond 0.04177 / 2.81 ( 537) hydrogen bonds : angle 5.70265 / 4.16 ( 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 257 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 205 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.4847 (p90) cc_final: 0.4612 (p90) REVERT: A 145 MET cc_start: 0.7137 (tpp) cc_final: 0.6869 (tpp) REVERT: A 172 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7725 (tt) REVERT: A 410 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6587 (mp0) REVERT: B 42 ASP cc_start: 0.7762 (m-30) cc_final: 0.7378 (t0) REVERT: B 104 ASN cc_start: 0.8278 (t0) cc_final: 0.8008 (t0) REVERT: B 187 ASP cc_start: 0.7751 (m-30) cc_final: 0.7460 (m-30) REVERT: C 84 GLU cc_start: 0.6840 (tt0) cc_final: 0.6315 (tt0) REVERT: C 145 MET cc_start: 0.9019 (tmm) cc_final: 0.8311 (tmm) REVERT: C 149 MET cc_start: 0.8320 (tpp) cc_final: 0.7878 (tpp) REVERT: C 246 ILE cc_start: 0.8845 (mm) cc_final: 0.8636 (tt) REVERT: C 269 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7317 (mm-30) REVERT: D 149 MET cc_start: 0.7935 (tpp) cc_final: 0.7615 (mpp) REVERT: D 174 THR cc_start: 0.8402 (p) cc_final: 0.8142 (t) outliers start: 52 outliers final: 28 residues processed: 243 average time/residue: 0.0853 time to fit residues: 32.5157 Evaluate side-chains 224 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 172 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 365 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 410 GLU 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 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 C residue 12 VAL 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 269 GLU Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain D residue 239 SER 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 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: 1.9990 chunk 60 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 145 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** C 305 GLN C 363 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 = 0.3728 r_free = 0.3728 target = 0.120029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.105019 restraints weight = 27375.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.108100 restraints weight = 14258.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.110173 restraints weight = 8795.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.111541 restraints weight = 6145.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.112460 restraints weight = 4725.957| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13756 Z= 0.175 Angle : 0.725 10.419 18860 Z= 0.351 Chirality : 0.050 0.359 2200 Planarity : 0.006 0.050 2464 Dihedral : 8.617 175.786 2048 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 22.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.92 % Favored : 94.03 % Rotamer: Outliers : 3.16 % Allowed : 18.75 % Favored : 78.09 % 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: -0.50 (0.20), residues: 1724 helix: 1.24 (0.21), residues: 572 sheet: -0.75 (0.29), residues: 336 loop : -1.28 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 277 TYR 0.030 0.002 TYR D 301 PHE 0.023 0.002 PHE D 98 TRP 0.025 0.002 TRP A 394 HIS 0.009 0.001 HIS D 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 (13756) covalent geometry : angle 0.72539 / 0.35 (18860) hydrogen bonds : bond 0.04007 / 2.70 ( 537) hydrogen bonds : angle 5.66572 / 4.13 ( 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 243 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 199 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.4851 (p90) cc_final: 0.4624 (p90) REVERT: A 145 MET cc_start: 0.7131 (tpp) cc_final: 0.6856 (tpp) REVERT: A 172 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7765 (tt) REVERT: B 104 ASN cc_start: 0.8250 (t0) cc_final: 0.8032 (t0) REVERT: B 187 ASP cc_start: 0.7585 (m-30) cc_final: 0.7307 (m-30) REVERT: C 84 GLU cc_start: 0.6852 (tt0) cc_final: 0.6406 (tt0) REVERT: C 145 MET cc_start: 0.9001 (tmm) cc_final: 0.8333 (tmm) REVERT: C 149 MET cc_start: 0.8341 (tpp) cc_final: 0.7955 (tpp) REVERT: C 246 ILE cc_start: 0.8794 (mm) cc_final: 0.8564 (tt) REVERT: D 174 THR cc_start: 0.8389 (p) cc_final: 0.8112 (t) outliers start: 44 outliers final: 28 residues processed: 227 average time/residue: 0.0941 time to fit residues: 33.3012 Evaluate side-chains 211 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU 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 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 401 ASP Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain C residue 12 VAL 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 242 ILE Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 280 ILE 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 365 VAL Chi-restraints excluded: chain D residue 398 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 158 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 ASN ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN A 315 ASN ** 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 305 GLN C 363 ASN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.121872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.106784 restraints weight = 27372.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.109913 restraints weight = 14094.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.112016 restraints weight = 8662.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.113414 restraints weight = 6036.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.114402 restraints weight = 4614.737| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13756 Z= 0.156 Angle : 0.724 10.691 18860 Z= 0.350 Chirality : 0.050 0.311 2200 Planarity : 0.006 0.048 2464 Dihedral : 8.523 172.168 2048 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 21.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.97 % Favored : 93.97 % Rotamer: Outliers : 3.59 % Allowed : 18.97 % Favored : 77.44 % 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: 1.38 (0.22), residues: 572 sheet: -0.80 (0.29), residues: 336 loop : -1.23 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 147 TYR 0.027 0.002 TYR D 301 PHE 0.029 0.002 PHE B 215 TRP 0.038 0.002 TRP A 394 HIS 0.009 0.001 HIS D 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (13756) covalent geometry : angle 0.72424 / 0.35 (18860) hydrogen bonds : bond 0.03907 / 2.63 ( 537) hydrogen bonds : angle 5.56969 / 4.06 ( 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 265 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 215 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7884 (tt) REVERT: B 187 ASP cc_start: 0.7554 (m-30) cc_final: 0.7287 (m-30) REVERT: B 346 ILE cc_start: 0.8243 (pt) cc_final: 0.8040 (pt) REVERT: C 84 GLU cc_start: 0.6828 (tt0) cc_final: 0.6388 (tt0) REVERT: C 120 ARG cc_start: 0.8570 (tmm-80) cc_final: 0.8337 (ptt90) REVERT: C 305 GLN cc_start: 0.6790 (OUTLIER) cc_final: 0.6467 (mm110) REVERT: C 371 ARG cc_start: 0.7547 (ttt90) cc_final: 0.6891 (ttt90) REVERT: D 145 MET cc_start: 0.8277 (tmm) cc_final: 0.7618 (tpp) REVERT: D 174 THR cc_start: 0.8353 (p) cc_final: 0.8066 (t) outliers start: 50 outliers final: 31 residues processed: 251 average time/residue: 0.0974 time to fit residues: 37.1656 Evaluate side-chains 226 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 172 LEU 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 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 376 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 401 ASP 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 242 ILE Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 305 GLN 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 281 VAL Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 398 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 29 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 69 optimal weight: 0.0770 chunk 35 optimal weight: 3.9990 chunk 166 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 overall best weight: 0.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 ASN ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 ASN ** 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 363 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.123375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.108284 restraints weight = 27169.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.111452 restraints weight = 14018.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.113580 restraints weight = 8585.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.114934 restraints weight = 5953.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.115957 restraints weight = 4568.670| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2918 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= 0.149 Angle : 0.729 10.580 18860 Z= 0.351 Chirality : 0.050 0.309 2200 Planarity : 0.006 0.086 2464 Dihedral : 8.493 172.602 2048 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.92 % Favored : 94.03 % Rotamer: Outliers : 3.16 % Allowed : 20.19 % Favored : 76.65 % 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: -0.38 (0.20), residues: 1724 helix: 1.45 (0.22), residues: 572 sheet: -0.86 (0.29), residues: 336 loop : -1.21 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 126 TYR 0.023 0.002 TYR B 316 PHE 0.027 0.002 PHE B 215 TRP 0.037 0.002 TRP A 394 HIS 0.007 0.001 HIS D 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (13756) covalent geometry : angle 0.72865 / 0.35 (18860) hydrogen bonds : bond 0.03839 / 2.56 ( 537) hydrogen bonds : angle 5.56297 / 4.06 ( 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 255 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 211 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.7100 (mtp180) cc_final: 0.4339 (tmt170) REVERT: A 424 ILE cc_start: 0.9152 (mm) cc_final: 0.8942 (mt) REVERT: B 28 LEU cc_start: 0.8924 (tt) cc_final: 0.8646 (tt) REVERT: B 346 ILE cc_start: 0.8159 (pt) cc_final: 0.7944 (pt) REVERT: C 84 GLU cc_start: 0.6819 (tt0) cc_final: 0.6383 (tt0) REVERT: C 371 ARG cc_start: 0.7460 (ttt90) cc_final: 0.6562 (ttt90) REVERT: C 404 PHE cc_start: 0.7805 (t80) cc_final: 0.7573 (t80) REVERT: D 174 THR cc_start: 0.8315 (p) cc_final: 0.8014 (t) outliers start: 44 outliers final: 35 residues processed: 243 average time/residue: 0.1003 time to fit residues: 37.1439 Evaluate side-chains 228 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 46 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 357 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 31 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 376 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 401 ASP 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 198 GLU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 412 ILE 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 281 VAL Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 398 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 2 optimal weight: 0.0270 chunk 108 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 116 optimal weight: 0.1980 chunk 69 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.124968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.110848 restraints weight = 26970.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.114032 restraints weight = 13552.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.116126 restraints weight = 8025.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.117501 restraints weight = 5406.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.118443 restraints weight = 4039.754| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13756 Z= 0.147 Angle : 0.734 11.001 18860 Z= 0.355 Chirality : 0.049 0.288 2200 Planarity : 0.006 0.072 2464 Dihedral : 8.454 172.926 2048 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.63 % Favored : 94.32 % Rotamer: Outliers : 2.95 % Allowed : 20.91 % Favored : 76.15 % 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: 1.43 (0.22), residues: 572 sheet: -0.88 (0.29), residues: 336 loop : -1.23 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 126 TYR 0.025 0.003 TYR B 409 PHE 0.031 0.002 PHE B 215 TRP 0.046 0.002 TRP A 394 HIS 0.007 0.001 HIS D 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (13756) covalent geometry : angle 0.73351 / 0.35 (18860) hydrogen bonds : bond 0.03746 / 2.50 ( 537) hydrogen bonds : angle 5.59361 / 4.09 ( 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 251 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 210 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.6952 (mtp180) cc_final: 0.4267 (tmt170) REVERT: A 424 ILE cc_start: 0.9125 (mm) cc_final: 0.8909 (mt) REVERT: B 215 PHE cc_start: 0.7749 (m-10) cc_final: 0.7229 (m-10) REVERT: C 84 GLU cc_start: 0.6816 (tt0) cc_final: 0.6379 (tt0) REVERT: C 371 ARG cc_start: 0.7368 (ttt90) cc_final: 0.6599 (ttt90) REVERT: C 404 PHE cc_start: 0.7808 (t80) cc_final: 0.7603 (t80) outliers start: 41 outliers final: 31 residues processed: 240 average time/residue: 0.1014 time to fit residues: 36.7543 Evaluate side-chains 224 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 46 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 357 LEU 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 376 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 401 ASP 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 198 GLU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 363 ASN Chi-restraints excluded: chain C residue 412 ILE 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 281 VAL Chi-restraints excluded: chain D residue 398 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 47 optimal weight: 0.5980 chunk 78 optimal weight: 0.0170 chunk 61 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 0.0470 chunk 24 optimal weight: 0.9990 chunk 120 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 ASN ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN A 315 ASN B 306 HIS ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.126606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.112366 restraints weight = 26754.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.115549 restraints weight = 13465.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.117668 restraints weight = 7980.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.119067 restraints weight = 5389.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.120044 restraints weight = 4023.246| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13756 Z= 0.141 Angle : 0.747 11.053 18860 Z= 0.360 Chirality : 0.049 0.271 2200 Planarity : 0.006 0.066 2464 Dihedral : 8.425 173.300 2048 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.73 % Allowed : 21.48 % Favored : 75.79 % 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: 1.18 (0.21), residues: 596 sheet: -0.88 (0.29), residues: 332 loop : -1.15 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 126 TYR 0.023 0.002 TYR B 409 PHE 0.018 0.002 PHE D 98 TRP 0.048 0.003 TRP A 394 HIS 0.006 0.001 HIS D 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (13756) covalent geometry : angle 0.74687 / 0.36 (18860) hydrogen bonds : bond 0.03688 / 2.46 ( 537) hydrogen bonds : angle 5.57279 / 4.07 ( 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 247 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 209 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.6824 (mtp180) cc_final: 0.4115 (tmt170) REVERT: B 139 ARG cc_start: 0.8103 (tpp80) cc_final: 0.7603 (tpp-160) REVERT: C 84 GLU cc_start: 0.6783 (tt0) cc_final: 0.6371 (tt0) REVERT: C 177 THR cc_start: 0.8621 (m) cc_final: 0.8330 (m) REVERT: C 371 ARG cc_start: 0.7334 (ttt90) cc_final: 0.6592 (ttt90) REVERT: D 151 TRP cc_start: 0.7375 (m-10) cc_final: 0.6831 (m-10) outliers start: 38 outliers final: 31 residues processed: 236 average time/residue: 0.0962 time to fit residues: 34.8518 Evaluate side-chains 224 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 46 LEU 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 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 376 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 401 ASP 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 198 GLU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 412 ILE 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 281 VAL Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 398 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 150 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 148 optimal weight: 0.0870 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 overall best weight: 2.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 ASN ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.118903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.103851 restraints weight = 27857.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.106904 restraints weight = 14428.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.108955 restraints weight = 8834.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.110332 restraints weight = 6157.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.111305 restraints weight = 4715.522| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13756 Z= 0.230 Angle : 0.798 11.638 18860 Z= 0.386 Chirality : 0.051 0.302 2200 Planarity : 0.006 0.053 2464 Dihedral : 8.528 173.234 2048 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 22.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.37 % Allowed : 22.05 % Favored : 75.57 % 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: -0.61 (0.20), residues: 1724 helix: 1.29 (0.22), residues: 572 sheet: -1.12 (0.28), residues: 336 loop : -1.31 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 147 TYR 0.028 0.003 TYR C 392 PHE 0.078 0.003 PHE B 215 TRP 0.066 0.003 TRP A 394 HIS 0.007 0.001 HIS A 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.23 (13756) covalent geometry : angle 0.79815 / 0.39 (18860) hydrogen bonds : bond 0.04029 / 2.71 ( 537) hydrogen bonds : angle 5.63787 / 4.11 ( 1569) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2012.79 seconds wall clock time: 35 minutes 43.65 seconds (2143.65 seconds total)