Starting phenix.real_space_refine on Mon Dec 30 15:59:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qqk_14122/12_2024/7qqk_14122.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qqk_14122/12_2024/7qqk_14122.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qqk_14122/12_2024/7qqk_14122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qqk_14122/12_2024/7qqk_14122.map" model { file = "/net/cci-nas-00/data/ceres_data/7qqk_14122/12_2024/7qqk_14122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qqk_14122/12_2024/7qqk_14122.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13444 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3295 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 399} Chain: "B" Number of atoms: 3295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3295 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 399} Chain: "C" Number of atoms: 3295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3295 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 399} Chain: "D" Number of atoms: 3295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3295 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 399} Chain: "E" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Chain: "F" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Chain: "G" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Chain: "H" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Time building chain proxies: 7.41, per 1000 atoms: 0.55 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: 3.33 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.96 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: 4.85 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4615 1.34 - 1.46: 2149 1.46 - 1.58: 6908 1.58 - 1.70: 20 1.70 - 1.82: 64 Bond restraints: 13756 Sorted by residual: bond pdb=" N VAL B 389 " pdb=" CA VAL B 389 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.17e-02 7.31e+03 8.60e+00 bond pdb=" N HIS C 18 " pdb=" CA HIS C 18 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.57e+00 bond pdb=" N TYR C 16 " pdb=" CA TYR C 16 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.29e-02 6.01e+03 6.46e+00 bond pdb=" N TYR B 392 " pdb=" CA TYR B 392 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.39e-02 5.18e+03 6.40e+00 bond pdb=" N ARG B 388 " pdb=" CA ARG B 388 " ideal model delta sigma weight residual 1.456 1.487 -0.030 1.21e-02 6.83e+03 6.34e+00 ... (remaining 13751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 18477 2.51 - 5.03: 339 5.03 - 7.54: 36 7.54 - 10.05: 6 10.05 - 12.56: 2 Bond angle restraints: 18860 Sorted by residual: angle pdb=" N ARG B 416 " pdb=" CA ARG B 416 " pdb=" C ARG B 416 " ideal model delta sigma weight residual 107.70 120.26 -12.56 2.09e+00 2.29e-01 3.61e+01 angle pdb=" N VAL C 251 " pdb=" CA VAL C 251 " pdb=" C VAL C 251 " ideal model delta sigma weight residual 106.42 114.02 -7.60 1.51e+00 4.39e-01 2.53e+01 angle pdb=" N ASP B 396 " pdb=" CA ASP B 396 " pdb=" C ASP B 396 " ideal model delta sigma weight residual 112.41 106.58 5.83 1.30e+00 5.92e-01 2.01e+01 angle pdb=" C HIS A 197 " pdb=" N GLU A 198 " pdb=" CA GLU A 198 " ideal model delta sigma weight residual 121.54 129.54 -8.00 1.91e+00 2.74e-01 1.76e+01 angle pdb=" N VAL B 390 " pdb=" CA VAL B 390 " pdb=" C VAL B 390 " ideal model delta sigma weight residual 108.17 102.33 5.84 1.40e+00 5.10e-01 1.74e+01 ... (remaining 18855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.50: 7662 19.50 - 39.00: 574 39.00 - 58.50: 67 58.50 - 78.00: 20 78.00 - 97.50: 9 Dihedral angle restraints: 8332 sinusoidal: 3352 harmonic: 4980 Sorted by residual: dihedral pdb=" CA ILE D 37 " pdb=" C ILE D 37 " pdb=" N PRO D 38 " pdb=" CA PRO D 38 " ideal model delta harmonic sigma weight residual 180.00 152.30 27.70 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA VAL C 251 " pdb=" C VAL C 251 " pdb=" N GLY C 252 " pdb=" CA GLY C 252 " ideal model delta harmonic sigma weight residual 180.00 154.92 25.08 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA ASP C 45 " pdb=" C ASP C 45 " pdb=" N LEU C 46 " pdb=" CA LEU C 46 " ideal model delta harmonic sigma weight residual 180.00 155.85 24.15 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 8329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1802 0.059 - 0.118: 356 0.118 - 0.176: 37 0.176 - 0.235: 4 0.235 - 0.294: 1 Chirality restraints: 2200 Sorted by residual: chirality pdb=" CA VAL B 390 " pdb=" N VAL B 390 " pdb=" C VAL B 390 " pdb=" CB VAL B 390 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CB THR C 285 " pdb=" CA THR C 285 " pdb=" OG1 THR C 285 " pdb=" CG2 THR C 285 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CG LEU B 338 " pdb=" CB LEU B 338 " pdb=" CD1 LEU B 338 " pdb=" CD2 LEU B 338 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.97e-01 ... (remaining 2197 not shown) Planarity restraints: 2464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 246 " 0.058 5.00e-02 4.00e+02 8.71e-02 1.21e+01 pdb=" N PRO A 247 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO A 247 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 247 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 1 " 0.044 5.00e-02 4.00e+02 6.57e-02 6.91e+00 pdb=" N PRO D 2 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO D 2 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 2 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 409 " -0.019 2.00e-02 2.50e+03 1.82e-02 6.60e+00 pdb=" CG TYR A 409 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 409 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 409 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR A 409 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 409 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR A 409 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 409 " -0.006 2.00e-02 2.50e+03 ... (remaining 2461 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 361 2.67 - 3.23: 14162 3.23 - 3.79: 23185 3.79 - 4.34: 30228 4.34 - 4.90: 48193 Nonbonded interactions: 116129 Sorted by model distance: nonbonded pdb=" O MET C 254 " pdb=" OG SER C 266 " model vdw 2.117 3.040 nonbonded pdb=" OG1 THR D 395 " pdb=" O ARG D 408 " model vdw 2.119 3.040 nonbonded pdb=" OP2 A E 1 " pdb=" O2' A E 3 " model vdw 2.131 3.040 nonbonded pdb=" OH TYR D 16 " pdb=" OD1 ASP D 42 " model vdw 2.151 3.040 nonbonded pdb=" OG SER C 171 " pdb=" OD1 ASP C 189 " model vdw 2.169 3.040 ... (remaining 116124 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 18.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 32.850 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13756 Z= 0.279 Angle : 0.814 12.563 18860 Z= 0.449 Chirality : 0.046 0.294 2200 Planarity : 0.006 0.087 2464 Dihedral : 13.773 97.499 5108 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 25.98 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.040 0.003 TRP A 327 HIS 0.010 0.001 HIS A 329 PHE 0.016 0.002 PHE C 215 TYR 0.039 0.003 TYR A 409 ARG 0.010 0.001 ARG D 382 *********************** 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 : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 359 MET cc_start: 0.3588 (tmm) cc_final: 0.2948 (tpt) REVERT: A 368 LEU cc_start: 0.8443 (tp) cc_final: 0.8229 (tt) REVERT: B 17 ARG cc_start: 0.6035 (mmt180) cc_final: 0.5631 (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: 0.7328 (t0) REVERT: B 145 MET cc_start: 0.8148 (tmm) cc_final: 0.7430 (tmm) REVERT: B 187 ASP cc_start: 0.7106 (m-30) cc_final: 0.6867 (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: 0.8273 (tt0) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.2475 time to fit residues: 99.9405 Evaluate side-chains 193 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 7.9990 chunk 130 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 81 optimal weight: 0.0170 chunk 100 optimal weight: 0.9980 chunk 156 optimal weight: 6.9990 overall best weight: 1.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN A 263 HIS A 305 GLN A 315 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** 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 361 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 GLN ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 ASN C 363 ASN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13756 Z= 0.276 Angle : 0.728 9.652 18860 Z= 0.360 Chirality : 0.046 0.166 2200 Planarity : 0.006 0.056 2464 Dihedral : 8.467 98.723 2048 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.45 % Favored : 94.37 % Rotamer: Outliers : 1.51 % Allowed : 11.14 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.20), residues: 1724 helix: 1.26 (0.21), residues: 572 sheet: -0.01 (0.30), residues: 328 loop : -1.32 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 394 HIS 0.011 0.001 HIS D 152 PHE 0.016 0.002 PHE B 404 TYR 0.022 0.002 TYR D 16 ARG 0.006 0.001 ARG C 408 *********************** 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 257 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 236 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 MET cc_start: 0.3828 (tmm) cc_final: 0.3195 (tpt) REVERT: A 393 GLU cc_start: 0.8429 (tp30) cc_final: 0.7717 (mm-30) REVERT: A 406 PRO cc_start: 0.8310 (Cg_exo) cc_final: 0.7762 (Cg_endo) REVERT: B 104 ASN cc_start: 0.7974 (t0) cc_final: 0.7680 (t0) REVERT: B 145 MET cc_start: 0.8192 (tmm) cc_final: 0.7833 (tmm) REVERT: B 187 ASP cc_start: 0.7351 (m-30) cc_final: 0.7060 (m-30) REVERT: B 202 SER cc_start: 0.8034 (OUTLIER) cc_final: 0.7772 (m) REVERT: C 84 GLU cc_start: 0.6961 (tt0) cc_final: 0.6552 (tt0) REVERT: C 361 ASN cc_start: 0.7728 (m-40) cc_final: 0.7424 (m110) REVERT: C 404 PHE cc_start: 0.7708 (t80) cc_final: 0.7246 (t80) REVERT: D 145 MET cc_start: 0.8049 (tmm) cc_final: 0.7749 (tpp) REVERT: D 149 MET cc_start: 0.7365 (tpp) cc_final: 0.6928 (mpp) REVERT: D 242 ILE cc_start: 0.8720 (tp) cc_final: 0.8474 (tt) outliers start: 21 outliers final: 10 residues processed: 249 average time/residue: 0.2536 time to fit residues: 93.3034 Evaluate side-chains 200 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 398 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 129 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 43 optimal weight: 10.9990 chunk 156 optimal weight: 6.9990 chunk 169 optimal weight: 4.9990 chunk 139 optimal weight: 0.5980 chunk 155 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN A 306 HIS A 315 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 GLN C 305 GLN C 353 HIS ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 13756 Z= 0.416 Angle : 0.769 8.210 18860 Z= 0.385 Chirality : 0.048 0.184 2200 Planarity : 0.007 0.054 2464 Dihedral : 8.602 94.233 2048 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 22.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.80 % Favored : 94.03 % Rotamer: Outliers : 2.80 % Allowed : 15.30 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.20), residues: 1724 helix: 1.07 (0.21), residues: 572 sheet: -0.69 (0.28), residues: 356 loop : -1.37 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 394 HIS 0.012 0.002 HIS D 152 PHE 0.014 0.002 PHE B 215 TYR 0.022 0.003 TYR D 16 ARG 0.006 0.001 ARG A 277 *********************** 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 246 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 207 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.8352 (tpp-160) cc_final: 0.8144 (tpp-160) REVERT: A 359 MET cc_start: 0.3718 (tmm) cc_final: 0.2962 (tpt) REVERT: A 410 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6039 (mp0) REVERT: B 104 ASN cc_start: 0.8267 (t0) cc_final: 0.7891 (t0) REVERT: B 187 ASP cc_start: 0.7768 (m-30) cc_final: 0.7453 (m-30) REVERT: C 60 ASP cc_start: 0.6912 (m-30) cc_final: 0.6676 (m-30) REVERT: C 84 GLU cc_start: 0.7128 (tt0) cc_final: 0.6604 (tt0) REVERT: C 404 PHE cc_start: 0.7903 (t80) cc_final: 0.7573 (t80) REVERT: C 412 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.8029 (mt) REVERT: D 145 MET cc_start: 0.8090 (tmm) cc_final: 0.7831 (tpp) REVERT: D 149 MET cc_start: 0.7808 (tpp) cc_final: 0.7508 (tpp) outliers start: 39 outliers final: 26 residues processed: 236 average time/residue: 0.2410 time to fit residues: 85.7805 Evaluate side-chains 207 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 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 202 SER Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 338 LEU 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 45 ASP Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 412 ILE 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 387 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 157 optimal weight: 8.9990 chunk 166 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN A 73 GLN ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN A 305 GLN A 315 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN B 305 GLN ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 ASN C 363 ASN C 385 ASN D 104 ASN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 GLN D 329 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13756 Z= 0.259 Angle : 0.693 9.641 18860 Z= 0.342 Chirality : 0.045 0.237 2200 Planarity : 0.006 0.046 2464 Dihedral : 8.509 96.649 2048 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 21.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.80 % Favored : 94.08 % Rotamer: Outliers : 3.59 % Allowed : 17.46 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.20), residues: 1724 helix: 1.00 (0.21), residues: 596 sheet: -0.65 (0.30), residues: 312 loop : -1.24 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 394 HIS 0.011 0.001 HIS D 152 PHE 0.030 0.002 PHE D 98 TYR 0.018 0.002 TYR D 16 ARG 0.007 0.000 ARG D 382 *********************** 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 274 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 224 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.8309 (tpp-160) cc_final: 0.8066 (tpp-160) REVERT: A 393 GLU cc_start: 0.8247 (tp30) cc_final: 0.7718 (mm-30) REVERT: B 42 ASP cc_start: 0.7838 (m-30) cc_final: 0.7445 (t0) REVERT: B 104 ASN cc_start: 0.8259 (t0) cc_final: 0.7980 (t0) REVERT: B 187 ASP cc_start: 0.7568 (m-30) cc_final: 0.7299 (m-30) REVERT: B 202 SER cc_start: 0.8188 (p) cc_final: 0.7916 (m) REVERT: C 84 GLU cc_start: 0.6804 (tt0) cc_final: 0.6314 (tt0) REVERT: C 145 MET cc_start: 0.8893 (tmm) cc_final: 0.8150 (tmm) REVERT: C 149 MET cc_start: 0.8054 (tpp) cc_final: 0.7707 (tpp) REVERT: C 404 PHE cc_start: 0.7868 (t80) cc_final: 0.7632 (t80) REVERT: D 145 MET cc_start: 0.7883 (tmm) cc_final: 0.7513 (tmm) outliers start: 50 outliers final: 28 residues processed: 259 average time/residue: 0.2415 time to fit residues: 93.4583 Evaluate side-chains 221 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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 315 ASN Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 366 VAL 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 337 LEU Chi-restraints excluded: chain B residue 338 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 206 LEU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 310 ASP Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 398 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 2 optimal weight: 0.0770 chunk 123 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 overall best weight: 0.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 GLN ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 ASN C 363 ASN C 367 HIS ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2368 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= 0.251 Angle : 0.700 10.778 18860 Z= 0.342 Chirality : 0.046 0.253 2200 Planarity : 0.006 0.054 2464 Dihedral : 8.360 95.151 2048 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.45 % Favored : 94.37 % Rotamer: Outliers : 3.38 % Allowed : 18.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.20), residues: 1724 helix: 1.03 (0.21), residues: 596 sheet: -0.68 (0.30), residues: 312 loop : -1.21 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 394 HIS 0.011 0.001 HIS D 329 PHE 0.025 0.002 PHE D 98 TYR 0.018 0.002 TYR D 16 ARG 0.007 0.000 ARG D 126 *********************** 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 268 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 221 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.8258 (tpp-160) cc_final: 0.8045 (tpp-160) REVERT: A 393 GLU cc_start: 0.8283 (tp30) cc_final: 0.7711 (mm-30) REVERT: B 104 ASN cc_start: 0.8259 (t0) cc_final: 0.8021 (t0) REVERT: B 187 ASP cc_start: 0.7548 (m-30) cc_final: 0.7272 (m-30) REVERT: C 84 GLU cc_start: 0.6802 (tt0) cc_final: 0.6309 (tt0) REVERT: C 145 MET cc_start: 0.8902 (tmm) cc_final: 0.8217 (tmm) REVERT: C 149 MET cc_start: 0.8086 (tpp) cc_final: 0.7755 (tpp) REVERT: C 269 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7007 (mm-30) REVERT: C 404 PHE cc_start: 0.7829 (t80) cc_final: 0.7629 (t80) outliers start: 47 outliers final: 27 residues processed: 255 average time/residue: 0.2510 time to fit residues: 94.4165 Evaluate side-chains 222 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain D residue 28 LEU 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 387 LEU 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 55 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 166 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN ** 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 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 ASN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 GLN ** D 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 13756 Z= 0.498 Angle : 0.814 11.392 18860 Z= 0.409 Chirality : 0.049 0.292 2200 Planarity : 0.007 0.067 2464 Dihedral : 8.668 101.417 2048 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 26.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.79 % Favored : 93.16 % Rotamer: Outliers : 3.88 % Allowed : 19.25 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.20), residues: 1724 helix: 0.90 (0.21), residues: 576 sheet: -1.20 (0.28), residues: 352 loop : -1.37 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP D 394 HIS 0.011 0.002 HIS D 152 PHE 0.025 0.002 PHE D 98 TYR 0.020 0.003 TYR D 16 ARG 0.006 0.001 ARG D 126 *********************** 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 245 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 191 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.8399 (tpp-160) cc_final: 0.8158 (tpp-160) REVERT: A 145 MET cc_start: 0.7370 (tpp) cc_final: 0.7065 (tpp) REVERT: A 393 GLU cc_start: 0.8522 (tp30) cc_final: 0.7841 (mm-30) REVERT: B 104 ASN cc_start: 0.8262 (t0) cc_final: 0.7978 (t0) REVERT: B 187 ASP cc_start: 0.7829 (m-30) cc_final: 0.7627 (m-30) REVERT: C 145 MET cc_start: 0.8995 (tmm) cc_final: 0.8536 (tmm) REVERT: C 269 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7001 (mm-30) REVERT: C 361 ASN cc_start: 0.7974 (m-40) cc_final: 0.7759 (m110) REVERT: C 371 ARG cc_start: 0.8350 (mtp-110) cc_final: 0.7959 (ttt90) outliers start: 54 outliers final: 44 residues processed: 232 average time/residue: 0.2271 time to fit residues: 81.0166 Evaluate side-chains 220 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 176 time to evaluate : 1.494 ------------------------------------------------------------------------------- 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 71 THR Chi-restraints excluded: chain A residue 132 VAL 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 324 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 79 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 365 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 408 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 165 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 HIS ** D 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2847 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= 0.269 Angle : 0.724 10.686 18860 Z= 0.357 Chirality : 0.047 0.317 2200 Planarity : 0.006 0.048 2464 Dihedral : 8.410 93.957 2048 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 22.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.68 % Favored : 94.26 % Rotamer: Outliers : 3.23 % Allowed : 20.69 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.20), residues: 1724 helix: 1.15 (0.21), residues: 572 sheet: -0.84 (0.31), residues: 304 loop : -1.27 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 394 HIS 0.010 0.001 HIS D 152 PHE 0.021 0.002 PHE D 98 TYR 0.021 0.002 TYR D 16 ARG 0.008 0.001 ARG D 126 *********************** 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 247 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 202 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9141 (tp) REVERT: A 393 GLU cc_start: 0.8303 (tp30) cc_final: 0.7415 (mm-30) REVERT: B 16 TYR cc_start: 0.7585 (p90) cc_final: 0.7188 (p90) REVERT: B 187 ASP cc_start: 0.7597 (m-30) cc_final: 0.7338 (m-30) REVERT: C 145 MET cc_start: 0.8921 (tmm) cc_final: 0.8467 (tmm) REVERT: C 269 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7084 (mm-30) REVERT: C 361 ASN cc_start: 0.7901 (m-40) cc_final: 0.7634 (m110) REVERT: C 404 PHE cc_start: 0.7908 (t80) cc_final: 0.7694 (t80) REVERT: D 369 MET cc_start: 0.7939 (tpp) cc_final: 0.7219 (mpp) outliers start: 45 outliers final: 32 residues processed: 236 average time/residue: 0.2433 time to fit residues: 85.9487 Evaluate side-chains 219 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 397 SER 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 280 ILE Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 408 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.0370 chunk 105 optimal weight: 0.5980 chunk 112 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 150 optimal weight: 0.0870 chunk 158 optimal weight: 0.0870 chunk 144 optimal weight: 1.9990 overall best weight: 0.3214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN A 315 ASN B 148 GLN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13756 Z= 0.230 Angle : 0.705 12.906 18860 Z= 0.344 Chirality : 0.046 0.296 2200 Planarity : 0.006 0.046 2464 Dihedral : 8.302 96.169 2048 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.86 % Favored : 94.08 % Rotamer: Outliers : 2.73 % Allowed : 22.27 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.20), residues: 1724 helix: 1.33 (0.22), residues: 572 sheet: -0.96 (0.28), residues: 340 loop : -1.20 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 394 HIS 0.013 0.001 HIS D 18 PHE 0.018 0.002 PHE D 98 TYR 0.022 0.002 TYR D 16 ARG 0.008 0.001 ARG D 126 *********************** 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 267 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 229 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.6635 (mmp80) cc_final: 0.6319 (mmp80) REVERT: A 355 ARG cc_start: 0.6935 (mtp180) cc_final: 0.4292 (tmt170) REVERT: B 28 LEU cc_start: 0.8917 (tt) cc_final: 0.8593 (tt) REVERT: B 139 ARG cc_start: 0.8137 (tpp80) cc_final: 0.7777 (tpp-160) REVERT: C 84 GLU cc_start: 0.7197 (tt0) cc_final: 0.6774 (pt0) REVERT: C 177 THR cc_start: 0.8601 (m) cc_final: 0.8337 (m) REVERT: C 269 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7031 (mm-30) REVERT: C 361 ASN cc_start: 0.7877 (m-40) cc_final: 0.7660 (m110) REVERT: C 371 ARG cc_start: 0.8213 (mtp-110) cc_final: 0.7858 (mtp-110) REVERT: C 394 TRP cc_start: 0.7394 (p-90) cc_final: 0.7176 (p-90) REVERT: C 404 PHE cc_start: 0.7918 (t80) cc_final: 0.7680 (t80) outliers start: 38 outliers final: 30 residues processed: 255 average time/residue: 0.2633 time to fit residues: 97.7171 Evaluate side-chains 226 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 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 298 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 408 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 2.9990 chunk 158 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 121 optimal weight: 0.9990 chunk 47 optimal weight: 0.0370 chunk 139 optimal weight: 10.0000 chunk 146 optimal weight: 0.0050 chunk 153 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 163 optimal weight: 8.9990 overall best weight: 1.0076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 ASN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3057 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= 0.262 Angle : 0.721 11.461 18860 Z= 0.350 Chirality : 0.047 0.298 2200 Planarity : 0.006 0.061 2464 Dihedral : 8.183 99.057 2048 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.21 % Favored : 93.68 % Rotamer: Outliers : 2.87 % Allowed : 22.05 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.20), residues: 1724 helix: 1.31 (0.21), residues: 572 sheet: -1.04 (0.28), residues: 340 loop : -1.19 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 394 HIS 0.012 0.001 HIS D 18 PHE 0.019 0.002 PHE A 215 TYR 0.022 0.002 TYR A 301 ARG 0.008 0.001 ARG D 147 *********************** 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 240 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 200 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.6614 (mmp80) cc_final: 0.6301 (mmp80) REVERT: A 31 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9085 (tp) REVERT: A 149 MET cc_start: 0.7451 (mtp) cc_final: 0.7229 (ttm) REVERT: A 175 ARG cc_start: 0.7977 (mtt-85) cc_final: 0.7742 (mtp85) REVERT: A 355 ARG cc_start: 0.6906 (mtp180) cc_final: 0.4307 (tmt170) REVERT: B 139 ARG cc_start: 0.8134 (tpp80) cc_final: 0.7786 (tpp-160) REVERT: C 84 GLU cc_start: 0.7191 (tt0) cc_final: 0.6736 (pt0) REVERT: C 177 THR cc_start: 0.8621 (m) cc_final: 0.8338 (m) REVERT: C 254 MET cc_start: 0.7565 (ttm) cc_final: 0.7255 (ttp) REVERT: C 269 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7073 (mm-30) REVERT: C 361 ASN cc_start: 0.7915 (m-40) cc_final: 0.7652 (m110) REVERT: C 371 ARG cc_start: 0.8215 (mtp-110) cc_final: 0.7876 (mtp-110) REVERT: C 394 TRP cc_start: 0.7530 (p-90) cc_final: 0.7156 (p-90) REVERT: C 404 PHE cc_start: 0.7978 (t80) cc_final: 0.7762 (t80) REVERT: D 149 MET cc_start: 0.7522 (mtp) cc_final: 0.7289 (mtt) outliers start: 40 outliers final: 34 residues processed: 230 average time/residue: 0.2496 time to fit residues: 85.9135 Evaluate side-chains 229 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 194 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 395 THR 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 206 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 408 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 108 optimal weight: 0.0980 chunk 145 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 ASN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 GLN ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13756 Z= 0.296 Angle : 0.731 12.081 18860 Z= 0.355 Chirality : 0.047 0.273 2200 Planarity : 0.006 0.049 2464 Dihedral : 8.134 100.332 2048 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.95 % Allowed : 21.98 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.20), residues: 1724 helix: 1.29 (0.21), residues: 572 sheet: -1.01 (0.29), residues: 304 loop : -1.26 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 394 HIS 0.010 0.001 HIS D 18 PHE 0.019 0.002 PHE D 98 TYR 0.026 0.002 TYR B 16 ARG 0.008 0.001 ARG C 355 ********************** 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 237 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 196 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.6656 (mmp80) cc_final: 0.6320 (mmp80) REVERT: A 31 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9082 (tp) REVERT: A 149 MET cc_start: 0.7579 (mtp) cc_final: 0.7357 (ttm) REVERT: A 175 ARG cc_start: 0.8070 (mtt-85) cc_final: 0.7793 (mtp85) REVERT: A 355 ARG cc_start: 0.6970 (mtp180) cc_final: 0.4358 (tmt170) REVERT: C 84 GLU cc_start: 0.7224 (tt0) cc_final: 0.6749 (pt0) REVERT: C 177 THR cc_start: 0.8649 (m) cc_final: 0.8351 (m) REVERT: C 269 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7088 (mm-30) REVERT: C 371 ARG cc_start: 0.8207 (mtp-110) cc_final: 0.7839 (mtp-110) REVERT: C 394 TRP cc_start: 0.7768 (p-90) cc_final: 0.7325 (p-90) outliers start: 41 outliers final: 35 residues processed: 226 average time/residue: 0.2452 time to fit residues: 83.7925 Evaluate side-chains 225 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 395 THR 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 206 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 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 280 ILE Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 408 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 0.0570 chunk 125 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 140 optimal weight: 0.0970 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 ASN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 GLN ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 HIS ** 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 = 0.3724 r_free = 0.3724 target = 0.120467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.106125 restraints weight = 27209.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.109107 restraints weight = 14047.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.111099 restraints weight = 8550.004| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.222 13756 Z= 0.358 Angle : 0.928 59.199 18860 Z= 0.508 Chirality : 0.050 0.951 2200 Planarity : 0.006 0.047 2464 Dihedral : 8.161 100.370 2048 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 24.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.50 % Favored : 93.45 % Rotamer: Outliers : 2.80 % Allowed : 22.70 % Favored : 74.50 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.20), residues: 1724 helix: 1.24 (0.21), residues: 572 sheet: -1.01 (0.29), residues: 304 loop : -1.26 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 394 HIS 0.007 0.001 HIS D 18 PHE 0.018 0.002 PHE D 98 TYR 0.021 0.002 TYR B 16 ARG 0.007 0.000 ARG C 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2860.48 seconds wall clock time: 55 minutes 5.32 seconds (3305.32 seconds total)