Starting phenix.real_space_refine on Sat Jul 4 11:45:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gmz_51458/07_2026/9gmz_51458.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gmz_51458/07_2026/9gmz_51458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gmz_51458/07_2026/9gmz_51458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gmz_51458/07_2026/9gmz_51458.map" model { file = "/net/cci-nas-00/data/ceres_data/9gmz_51458/07_2026/9gmz_51458.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gmz_51458/07_2026/9gmz_51458.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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: 6 Type Number sf(0) Gaussians P 51 5.49 5 Mg 7 5.21 5 S 56 5.16 5 C 12902 2.51 5 N 3571 2.21 5 O 3885 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20472 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2688 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 13, 'TRANS': 319} Chain: "B" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2755 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "C" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2755 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "D" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2755 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "E" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2755 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "F" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2755 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "G" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2755 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "H" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 64 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "I" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 64 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "J" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 64 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "K" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 64 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "L" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 64 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "M" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 64 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "1" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 323 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "2" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 323 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.84, per 1000 atoms: 0.24 Number of scatterers: 20472 At special positions: 0 Unit cell: (97.5, 150.8, 150.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 51 15.00 Mg 7 11.99 O 3885 8.00 N 3571 7.00 C 12902 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 815.4 milliseconds 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4604 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 10 sheets defined 63.3% alpha, 6.7% beta 16 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 8 through 14 Processing helix chain 'A' and resid 15 through 26 Processing helix chain 'A' and resid 30 through 46 Processing helix chain 'A' and resid 62 through 85 Proline residue: A 80 - end of helix removed outlier: 4.102A pdb=" N SER A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 117 Processing helix chain 'A' and resid 121 through 125 Processing helix chain 'A' and resid 148 through 164 Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 184 through 200 removed outlier: 4.209A pdb=" N GLN A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP A 190 " --> pdb=" O GLN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 removed outlier: 4.377A pdb=" N PHE A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 224 removed outlier: 3.798A pdb=" N SER A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 255 Processing helix chain 'A' and resid 266 through 275 Processing helix chain 'A' and resid 277 through 296 Processing helix chain 'A' and resid 301 through 309 removed outlier: 3.665A pdb=" N ARG A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 330 Processing helix chain 'B' and resid 8 through 13 Processing helix chain 'B' and resid 15 through 26 Processing helix chain 'B' and resid 30 through 46 Processing helix chain 'B' and resid 62 through 83 Proline residue: B 80 - end of helix Processing helix chain 'B' and resid 105 through 117 Processing helix chain 'B' and resid 121 through 125 removed outlier: 3.575A pdb=" N HIS B 124 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 164 Processing helix chain 'B' and resid 172 through 178 Processing helix chain 'B' and resid 183 through 200 removed outlier: 4.279A pdb=" N ASP B 187 " --> pdb=" O TYR B 183 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU B 192 " --> pdb=" O GLN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 215 removed outlier: 3.831A pdb=" N THR B 213 " --> pdb=" O GLU B 210 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG B 215 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 224 Processing helix chain 'B' and resid 237 through 255 Processing helix chain 'B' and resid 266 through 273 Processing helix chain 'B' and resid 277 through 296 Processing helix chain 'B' and resid 301 through 308 Processing helix chain 'B' and resid 311 through 329 Processing helix chain 'B' and resid 332 through 344 Processing helix chain 'C' and resid 8 through 14 Processing helix chain 'C' and resid 15 through 26 Processing helix chain 'C' and resid 30 through 46 Processing helix chain 'C' and resid 62 through 79 Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.702A pdb=" N GLU C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 117 Processing helix chain 'C' and resid 121 through 126 removed outlier: 4.250A pdb=" N LYS C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 164 Processing helix chain 'C' and resid 172 through 178 Processing helix chain 'C' and resid 183 through 200 removed outlier: 4.114A pdb=" N ASP C 187 " --> pdb=" O TYR C 183 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU C 192 " --> pdb=" O GLN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 215 removed outlier: 3.526A pdb=" N THR C 213 " --> pdb=" O GLU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 224 Processing helix chain 'C' and resid 237 through 255 Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'C' and resid 266 through 273 Processing helix chain 'C' and resid 277 through 295 removed outlier: 3.821A pdb=" N ARG C 295 " --> pdb=" O ASP C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 308 removed outlier: 3.743A pdb=" N ARG C 308 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 329 removed outlier: 3.515A pdb=" N LYS C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 343 removed outlier: 3.612A pdb=" N VAL C 336 " --> pdb=" O THR C 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 13 Processing helix chain 'D' and resid 15 through 26 removed outlier: 3.507A pdb=" N ARG D 19 " --> pdb=" O PRO D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 46 Processing helix chain 'D' and resid 62 through 83 removed outlier: 3.782A pdb=" N LEU D 77 " --> pdb=" O LYS D 73 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 79 " --> pdb=" O THR D 75 " (cutoff:3.500A) Proline residue: D 80 - end of helix removed outlier: 3.900A pdb=" N GLU D 83 " --> pdb=" O LEU D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 116 Processing helix chain 'D' and resid 121 through 126 removed outlier: 4.186A pdb=" N LYS D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 164 Processing helix chain 'D' and resid 172 through 178 removed outlier: 3.694A pdb=" N HIS D 175 " --> pdb=" O GLU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 200 removed outlier: 4.687A pdb=" N ASP D 187 " --> pdb=" O TYR D 183 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 189 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU D 192 " --> pdb=" O GLN D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 215 Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 237 through 255 Processing helix chain 'D' and resid 263 through 265 No H-bonds generated for 'chain 'D' and resid 263 through 265' Processing helix chain 'D' and resid 266 through 273 Processing helix chain 'D' and resid 277 through 295 removed outlier: 3.863A pdb=" N ARG D 295 " --> pdb=" O ASP D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 308 removed outlier: 3.593A pdb=" N ARG D 308 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 330 Processing helix chain 'D' and resid 332 through 343 Processing helix chain 'E' and resid 8 through 14 Processing helix chain 'E' and resid 15 through 26 Processing helix chain 'E' and resid 30 through 46 Processing helix chain 'E' and resid 62 through 79 Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing helix chain 'E' and resid 105 through 117 Processing helix chain 'E' and resid 121 through 125 removed outlier: 3.766A pdb=" N HIS E 124 " --> pdb=" O LEU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 164 Processing helix chain 'E' and resid 172 through 178 Processing helix chain 'E' and resid 183 through 200 removed outlier: 3.937A pdb=" N ASP E 187 " --> pdb=" O TYR E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 215 removed outlier: 3.518A pdb=" N THR E 213 " --> pdb=" O GLU E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 224 Processing helix chain 'E' and resid 237 through 254 Processing helix chain 'E' and resid 263 through 265 No H-bonds generated for 'chain 'E' and resid 263 through 265' Processing helix chain 'E' and resid 266 through 275 Processing helix chain 'E' and resid 277 through 295 removed outlier: 3.700A pdb=" N ARG E 295 " --> pdb=" O ASP E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 308 removed outlier: 3.575A pdb=" N ARG E 308 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 329 Processing helix chain 'E' and resid 332 through 344 removed outlier: 3.583A pdb=" N VAL E 336 " --> pdb=" O THR E 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 13 Processing helix chain 'F' and resid 15 through 26 Processing helix chain 'F' and resid 30 through 46 removed outlier: 3.504A pdb=" N GLU F 46 " --> pdb=" O ARG F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 79 Processing helix chain 'F' and resid 80 through 85 removed outlier: 4.138A pdb=" N GLU F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 117 removed outlier: 3.795A pdb=" N TYR F 109 " --> pdb=" O ASN F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 125 Processing helix chain 'F' and resid 148 through 164 Processing helix chain 'F' and resid 172 through 178 Processing helix chain 'F' and resid 183 through 200 removed outlier: 3.889A pdb=" N ASP F 187 " --> pdb=" O TYR F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 215 removed outlier: 4.005A pdb=" N THR F 213 " --> pdb=" O GLU F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 224 Processing helix chain 'F' and resid 237 through 253 Processing helix chain 'F' and resid 266 through 275 Processing helix chain 'F' and resid 277 through 296 Processing helix chain 'F' and resid 301 through 308 removed outlier: 4.024A pdb=" N ARG F 308 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 328 removed outlier: 3.953A pdb=" N GLN F 328 " --> pdb=" O GLU F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 343 Processing helix chain 'G' and resid 8 through 14 Processing helix chain 'G' and resid 15 through 26 Processing helix chain 'G' and resid 30 through 46 Processing helix chain 'G' and resid 62 through 83 Proline residue: G 80 - end of helix Processing helix chain 'G' and resid 105 through 116 Processing helix chain 'G' and resid 121 through 125 removed outlier: 3.959A pdb=" N HIS G 124 " --> pdb=" O LEU G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 164 Processing helix chain 'G' and resid 172 through 178 Processing helix chain 'G' and resid 184 through 200 Processing helix chain 'G' and resid 208 through 215 removed outlier: 3.610A pdb=" N LEU G 211 " --> pdb=" O THR G 208 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR G 213 " --> pdb=" O GLU G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 224 Processing helix chain 'G' and resid 237 through 255 Processing helix chain 'G' and resid 262 through 265 Processing helix chain 'G' and resid 266 through 275 Processing helix chain 'G' and resid 277 through 296 Processing helix chain 'G' and resid 301 through 308 removed outlier: 4.055A pdb=" N ARG G 308 " --> pdb=" O ASP G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 311 through 330 Processing helix chain 'G' and resid 332 through 344 removed outlier: 3.500A pdb=" N VAL G 336 " --> pdb=" O THR G 332 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 95 removed outlier: 6.770A pdb=" N VAL A 92 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ASP A 171 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE A 94 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE A 168 " --> pdb=" O CYS A 204 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LEU A 206 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL A 170 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE A 53 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N GLY A 207 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL A 55 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 91 through 95 removed outlier: 6.776A pdb=" N VAL B 92 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ASP B 171 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE B 94 " --> pdb=" O ASP B 171 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N PHE B 168 " --> pdb=" O CYS B 204 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LEU B 206 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL B 170 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ILE B 53 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLY B 207 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL B 55 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE B 52 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ILE B 228 " --> pdb=" O PHE B 52 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N PHE B 54 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE B 230 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TYR B 56 " --> pdb=" O PHE B 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 91 through 95 removed outlier: 3.517A pdb=" N VAL C 92 " --> pdb=" O VAL C 167 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE C 168 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU C 206 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL C 170 " --> pdb=" O LEU C 206 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 133 through 135 removed outlier: 3.556A pdb=" N SER C 134 " --> pdb=" O ASN C 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 91 through 95 removed outlier: 6.752A pdb=" N VAL D 92 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ASP D 171 " --> pdb=" O VAL D 92 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE D 94 " --> pdb=" O ASP D 171 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N PHE D 168 " --> pdb=" O CYS D 204 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU D 206 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL D 170 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE D 53 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N GLY D 207 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N VAL D 55 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N PHE D 52 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ILE D 228 " --> pdb=" O PHE D 52 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N PHE D 54 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE D 230 " --> pdb=" O PHE D 54 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR D 56 " --> pdb=" O PHE D 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 134 through 135 Processing sheet with id=AA7, first strand: chain 'E' and resid 91 through 95 removed outlier: 6.543A pdb=" N VAL E 92 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ASP E 171 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE E 94 " --> pdb=" O ASP E 171 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ILE E 53 " --> pdb=" O LEU E 205 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N GLY E 207 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL E 55 " --> pdb=" O GLY E 207 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 133 through 135 removed outlier: 3.601A pdb=" N SER E 134 " --> pdb=" O ASN E 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 91 through 95 removed outlier: 6.833A pdb=" N VAL F 92 " --> pdb=" O PHE F 169 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ASP F 171 " --> pdb=" O VAL F 92 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE F 94 " --> pdb=" O ASP F 171 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE F 168 " --> pdb=" O CYS F 204 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU F 206 " --> pdb=" O PHE F 168 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL F 170 " --> pdb=" O LEU F 206 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ILE F 53 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLY F 207 " --> pdb=" O ILE F 53 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL F 55 " --> pdb=" O GLY F 207 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N PHE F 52 " --> pdb=" O VAL F 226 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE F 228 " --> pdb=" O PHE F 52 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N PHE F 54 " --> pdb=" O ILE F 228 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N PHE F 230 " --> pdb=" O PHE F 54 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N TYR F 56 " --> pdb=" O PHE F 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 91 through 95 removed outlier: 6.583A pdb=" N VAL G 92 " --> pdb=" O PHE G 169 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ASP G 171 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE G 94 " --> pdb=" O ASP G 171 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE G 168 " --> pdb=" O CYS G 204 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LEU G 206 " --> pdb=" O PHE G 168 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL G 170 " --> pdb=" O LEU G 206 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE G 53 " --> pdb=" O LEU G 205 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLY G 207 " --> pdb=" O ILE G 53 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL G 55 " --> pdb=" O GLY G 207 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N PHE G 52 " --> pdb=" O VAL G 226 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ILE G 228 " --> pdb=" O PHE G 52 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N PHE G 54 " --> pdb=" O ILE G 228 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 1038 hydrogen bonds defined for protein. 2853 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 3.49 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3318 1.31 - 1.44: 5746 1.44 - 1.56: 11719 1.56 - 1.68: 81 1.68 - 1.81: 91 Bond restraints: 20955 Sorted by residual: bond pdb=" CA GLU D 172 " pdb=" C GLU D 172 " ideal model delta sigma weight residual 1.530 1.457 0.073 1.17e-02 7.31e+03 3.93e+01 bond pdb=" CA TYR B 271 " pdb=" C TYR B 271 " ideal model delta sigma weight residual 1.524 1.459 0.065 1.29e-02 6.01e+03 2.51e+01 bond pdb=" CA GLU B 272 " pdb=" C GLU B 272 " ideal model delta sigma weight residual 1.524 1.461 0.063 1.32e-02 5.74e+03 2.25e+01 bond pdb=" CA VAL K 893 " pdb=" C VAL K 893 " ideal model delta sigma weight residual 1.526 1.487 0.039 1.04e-02 9.25e+03 1.39e+01 bond pdb=" CA ASN G 105 " pdb=" C ASN G 105 " ideal model delta sigma weight residual 1.524 1.480 0.044 1.27e-02 6.20e+03 1.22e+01 ... (remaining 20950 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 28140 2.33 - 4.66: 345 4.66 - 6.99: 33 6.99 - 9.32: 20 9.32 - 11.65: 6 Bond angle restraints: 28544 Sorted by residual: angle pdb=" N VAL E 61 " pdb=" CA VAL E 61 " pdb=" C VAL E 61 " ideal model delta sigma weight residual 110.72 119.36 -8.64 1.01e+00 9.80e-01 7.32e+01 angle pdb=" N ARG D 215 " pdb=" CA ARG D 215 " pdb=" C ARG D 215 " ideal model delta sigma weight residual 111.40 120.18 -8.78 1.22e+00 6.72e-01 5.18e+01 angle pdb=" N VAL L 893 " pdb=" CA VAL L 893 " pdb=" C VAL L 893 " ideal model delta sigma weight residual 108.11 117.83 -9.72 1.40e+00 5.10e-01 4.83e+01 angle pdb=" N VAL J 893 " pdb=" CA VAL J 893 " pdb=" C VAL J 893 " ideal model delta sigma weight residual 108.11 115.99 -7.88 1.40e+00 5.10e-01 3.17e+01 angle pdb=" N PRO G 90 " pdb=" CA PRO G 90 " pdb=" C PRO G 90 " ideal model delta sigma weight residual 113.53 121.07 -7.54 1.39e+00 5.18e-01 2.94e+01 ... (remaining 28539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.07: 11426 23.07 - 46.15: 985 46.15 - 69.22: 187 69.22 - 92.29: 35 92.29 - 115.37: 3 Dihedral angle restraints: 12636 sinusoidal: 5515 harmonic: 7121 Sorted by residual: dihedral pdb=" CA THR G 116 " pdb=" C THR G 116 " pdb=" N LEU G 117 " pdb=" CA LEU G 117 " ideal model delta harmonic sigma weight residual 180.00 158.05 21.95 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" C VAL E 61 " pdb=" N VAL E 61 " pdb=" CA VAL E 61 " pdb=" CB VAL E 61 " ideal model delta harmonic sigma weight residual -122.00 -132.61 10.61 0 2.50e+00 1.60e-01 1.80e+01 dihedral pdb=" C VAL C 61 " pdb=" N VAL C 61 " pdb=" CA VAL C 61 " pdb=" CB VAL C 61 " ideal model delta harmonic sigma weight residual -122.00 -131.88 9.88 0 2.50e+00 1.60e-01 1.56e+01 ... (remaining 12633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2951 0.087 - 0.174: 225 0.174 - 0.261: 11 0.261 - 0.348: 7 0.348 - 0.435: 3 Chirality restraints: 3197 Sorted by residual: chirality pdb=" CA ARG C 340 " pdb=" N ARG C 340 " pdb=" C ARG C 340 " pdb=" CB ARG C 340 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CA PRO G 90 " pdb=" N PRO G 90 " pdb=" C PRO G 90 " pdb=" CB PRO G 90 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CA ALA G 98 " pdb=" N ALA G 98 " pdb=" C ALA G 98 " pdb=" CB ALA G 98 " both_signs ideal model delta sigma weight residual False 2.48 2.13 0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 3194 not shown) Planarity restraints: 3523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 101 " -0.023 2.00e-02 2.50e+03 4.64e-02 2.16e+01 pdb=" C SER C 101 " 0.080 2.00e-02 2.50e+03 pdb=" O SER C 101 " -0.030 2.00e-02 2.50e+03 pdb=" N ARG C 102 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA G 98 " 0.052 5.00e-02 4.00e+02 7.78e-02 9.69e+00 pdb=" N PRO G 99 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO G 99 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 99 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 126 " 0.018 2.00e-02 2.50e+03 1.69e-02 4.99e+00 pdb=" CG PHE G 126 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE G 126 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE G 126 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE G 126 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE G 126 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE G 126 " -0.001 2.00e-02 2.50e+03 ... (remaining 3520 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 145 2.52 - 3.11: 15279 3.11 - 3.71: 33283 3.71 - 4.30: 45166 4.30 - 4.90: 75082 Nonbonded interactions: 168955 Sorted by model distance: nonbonded pdb=" O1B ANP C 401 " pdb="MG MG C 402 " model vdw 1.922 2.170 nonbonded pdb=" O1B ANP F 401 " pdb="MG MG F 402 " model vdw 1.941 2.170 nonbonded pdb=" O1G ANP F 401 " pdb="MG MG F 402 " model vdw 1.972 2.170 nonbonded pdb=" O1B ANP B 401 " pdb="MG MG B 402 " model vdw 1.998 2.170 nonbonded pdb=" O1B ANP D 401 " pdb="MG MG D 402 " model vdw 2.016 2.170 ... (remaining 168950 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 '1' and resid 1 through 14) selection = (chain '2' and ((resid -14 and (name C4' or name O4' or name C3' or name O3' or \ name C2' or name C1' or name N9 or name C8 or name N7 or name C5 or name C6 or n \ ame N6 or name N1 or name C2 or name N3 or name C4 )) or resid -13 through -1)) } ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 5 through 337 or resid 401 through 402)) selection = (chain 'C' and (resid 5 through 337 or resid 401 through 402)) selection = (chain 'D' and (resid 5 through 337 or resid 401 through 402)) selection = (chain 'E' and (resid 5 through 337 or resid 401 through 402)) selection = (chain 'F' and (resid 5 through 337 or resid 401 through 402)) selection = (chain 'G' and (resid 5 through 337 or resid 401 through 402)) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.190 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 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 0.073 20955 Z= 0.249 Angle : 0.654 11.650 28544 Z= 0.397 Chirality : 0.047 0.435 3197 Planarity : 0.004 0.078 3523 Dihedral : 17.085 115.366 8032 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.38 % Allowed : 14.42 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.18), residues: 2407 helix: 1.71 (0.14), residues: 1430 sheet: 0.44 (0.40), residues: 196 loop : 0.29 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 153 TYR 0.034 0.001 TYR G 110 PHE 0.038 0.001 PHE G 126 TRP 0.006 0.001 TRP C 284 HIS 0.003 0.001 HIS G 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.25 (20955) covalent geometry : angle 0.65379 / 0.40 (28544) hydrogen bonds : bond 0.16020 / 10.12 ( 1078) hydrogen bonds : angle 4.63898 / 3.37 ( 2933) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8586 (p90) cc_final: 0.8171 (t80) REVERT: A 142 ASN cc_start: 0.8021 (m110) cc_final: 0.7586 (m110) REVERT: A 164 HIS cc_start: 0.8787 (t-90) cc_final: 0.8097 (t-90) REVERT: A 198 MET cc_start: 0.8051 (mtm) cc_final: 0.7653 (ptp) REVERT: A 267 TRP cc_start: 0.9008 (p-90) cc_final: 0.8725 (p-90) REVERT: A 328 GLN cc_start: 0.8299 (mt0) cc_final: 0.8012 (mp10) REVERT: B 35 GLU cc_start: 0.8851 (tt0) cc_final: 0.8461 (tm-30) REVERT: B 73 LYS cc_start: 0.9019 (tptm) cc_final: 0.8624 (tppt) REVERT: B 227 ASP cc_start: 0.8832 (m-30) cc_final: 0.8353 (p0) REVERT: C 34 LYS cc_start: 0.9324 (mmmt) cc_final: 0.8887 (mtpt) REVERT: C 69 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8072 (tpp80) REVERT: C 121 LEU cc_start: 0.8937 (mp) cc_final: 0.8579 (pp) REVERT: C 137 ASN cc_start: 0.8956 (t0) cc_final: 0.8588 (t0) REVERT: C 198 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8539 (mtm) REVERT: C 307 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8649 (mmtp) REVERT: D 14 ARG cc_start: 0.8786 (mmm160) cc_final: 0.8158 (mmm160) REVERT: D 24 GLU cc_start: 0.9304 (tp30) cc_final: 0.8954 (tp30) REVERT: D 164 HIS cc_start: 0.8239 (t-170) cc_final: 0.7888 (t-170) REVERT: E 56 TYR cc_start: 0.8614 (OUTLIER) cc_final: 0.7633 (p90) REVERT: E 94 ILE cc_start: 0.9051 (tp) cc_final: 0.8761 (pt) REVERT: E 102 ARG cc_start: 0.8146 (mtt-85) cc_final: 0.7320 (ttp-110) REVERT: E 103 TYR cc_start: 0.7912 (p90) cc_final: 0.7654 (p90) REVERT: E 262 ASN cc_start: 0.8798 (t0) cc_final: 0.8389 (t0) REVERT: F 119 GLU cc_start: 0.6618 (tp30) cc_final: 0.6356 (pt0) REVERT: F 140 LYS cc_start: 0.7522 (ptpt) cc_final: 0.6534 (tmmt) REVERT: F 142 ASN cc_start: 0.9288 (p0) cc_final: 0.8584 (p0) REVERT: G 41 MET cc_start: 0.9349 (tpt) cc_final: 0.9079 (tpt) REVERT: G 198 MET cc_start: 0.9200 (mtm) cc_final: 0.8876 (mtm) REVERT: G 270 PHE cc_start: 0.8821 (m-80) cc_final: 0.8557 (m-80) REVERT: G 271 TYR cc_start: 0.7656 (t80) cc_final: 0.7303 (t80) REVERT: G 303 LYS cc_start: 0.9094 (tppt) cc_final: 0.8871 (mmtp) REVERT: H 898 PHE cc_start: 0.6818 (t80) cc_final: 0.6427 (t80) outliers start: 29 outliers final: 14 residues processed: 190 average time/residue: 0.1668 time to fit residues: 48.4303 Evaluate side-chains 158 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 323 GLN Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain L residue 893 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 ASN ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 HIS D 242 GLN E 216 ASN E 242 GLN G 105 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.080975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.056337 restraints weight = 56531.916| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.60 r_work: 0.2811 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20955 Z= 0.222 Angle : 0.616 9.467 28544 Z= 0.310 Chirality : 0.043 0.236 3197 Planarity : 0.004 0.058 3523 Dihedral : 13.452 117.986 3301 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.48 % Allowed : 14.56 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.18), residues: 2407 helix: 1.47 (0.14), residues: 1472 sheet: 0.28 (0.39), residues: 196 loop : 0.44 (0.24), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 69 TYR 0.013 0.001 TYR D 37 PHE 0.023 0.002 PHE D 319 TRP 0.012 0.001 TRP C 284 HIS 0.004 0.001 HIS G 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.22 (20955) covalent geometry : angle 0.61609 / 0.31 (28544) hydrogen bonds : bond 0.04553 / 2.98 ( 1078) hydrogen bonds : angle 4.03528 / 2.90 ( 2933) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 145 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8533 (p90) cc_final: 0.8118 (t80) REVERT: A 142 ASN cc_start: 0.8093 (m110) cc_final: 0.7638 (m110) REVERT: A 164 HIS cc_start: 0.8726 (t-90) cc_final: 0.7991 (t-90) REVERT: A 198 MET cc_start: 0.7973 (mtm) cc_final: 0.7496 (ptp) REVERT: A 328 GLN cc_start: 0.8312 (mt0) cc_final: 0.8040 (mp10) REVERT: B 35 GLU cc_start: 0.8925 (tt0) cc_final: 0.8559 (tm-30) REVERT: B 73 LYS cc_start: 0.9077 (tptm) cc_final: 0.8660 (tppt) REVERT: B 137 ASN cc_start: 0.7821 (t0) cc_final: 0.7351 (p0) REVERT: B 220 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7704 (tp40) REVERT: B 227 ASP cc_start: 0.8817 (m-30) cc_final: 0.8395 (p0) REVERT: C 34 LYS cc_start: 0.9332 (mmmt) cc_final: 0.8970 (mtpt) REVERT: C 121 LEU cc_start: 0.8928 (mp) cc_final: 0.8616 (pp) REVERT: C 137 ASN cc_start: 0.8940 (t0) cc_final: 0.8513 (p0) REVERT: C 198 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8358 (mtm) REVERT: C 221 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8878 (mm) REVERT: C 307 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8887 (tppt) REVERT: D 24 GLU cc_start: 0.9349 (tp30) cc_final: 0.8961 (tp30) REVERT: E 56 TYR cc_start: 0.8718 (OUTLIER) cc_final: 0.7766 (p90) REVERT: E 102 ARG cc_start: 0.8319 (mtt-85) cc_final: 0.7493 (ttp-110) REVERT: E 103 TYR cc_start: 0.8007 (p90) cc_final: 0.7743 (p90) REVERT: E 105 ASN cc_start: 0.9098 (t0) cc_final: 0.8845 (t0) REVERT: E 210 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8576 (mp0) REVERT: E 262 ASN cc_start: 0.8791 (t0) cc_final: 0.8470 (t0) REVERT: F 119 GLU cc_start: 0.6729 (tp30) cc_final: 0.6493 (pt0) REVERT: F 140 LYS cc_start: 0.7561 (ptpt) cc_final: 0.6607 (tmmt) REVERT: F 142 ASN cc_start: 0.9301 (p0) cc_final: 0.8501 (p0) REVERT: F 172 GLU cc_start: 0.8566 (mm-30) cc_final: 0.7969 (mt-10) REVERT: G 41 MET cc_start: 0.9372 (tpt) cc_final: 0.9098 (tpt) REVERT: G 271 TYR cc_start: 0.7917 (t80) cc_final: 0.7559 (t80) REVERT: H 898 PHE cc_start: 0.7142 (t80) cc_final: 0.6785 (t80) REVERT: I 893 VAL cc_start: 0.8334 (t) cc_final: 0.8029 (p) REVERT: M 893 VAL cc_start: 0.8338 (m) cc_final: 0.8116 (p) outliers start: 52 outliers final: 25 residues processed: 184 average time/residue: 0.1663 time to fit residues: 47.0070 Evaluate side-chains 165 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain L residue 893 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 18 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 186 optimal weight: 2.9990 chunk 203 optimal weight: 10.0000 chunk 200 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.081137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.056654 restraints weight = 56187.792| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.61 r_work: 0.2791 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20955 Z= 0.143 Angle : 0.519 8.612 28544 Z= 0.265 Chirality : 0.040 0.172 3197 Planarity : 0.004 0.058 3523 Dihedral : 13.232 115.005 3287 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.33 % Allowed : 15.04 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.18), residues: 2407 helix: 1.59 (0.14), residues: 1465 sheet: 0.14 (0.39), residues: 196 loop : 0.52 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 14 TYR 0.030 0.001 TYR G 110 PHE 0.015 0.001 PHE F 138 TRP 0.012 0.001 TRP F 284 HIS 0.003 0.001 HIS G 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (20955) covalent geometry : angle 0.51944 / 0.26 (28544) hydrogen bonds : bond 0.04107 / 2.69 ( 1078) hydrogen bonds : angle 3.71958 / 2.67 ( 2933) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 139 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8494 (p90) cc_final: 0.8149 (t80) REVERT: A 142 ASN cc_start: 0.8084 (m110) cc_final: 0.7614 (m110) REVERT: A 164 HIS cc_start: 0.8765 (t-90) cc_final: 0.8098 (t-90) REVERT: A 198 MET cc_start: 0.7935 (mtm) cc_final: 0.7440 (ptp) REVERT: A 328 GLN cc_start: 0.8301 (mt0) cc_final: 0.8040 (mp10) REVERT: B 73 LYS cc_start: 0.9072 (tptm) cc_final: 0.8646 (tppt) REVERT: B 137 ASN cc_start: 0.7834 (t0) cc_final: 0.7481 (p0) REVERT: B 220 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7671 (tp40) REVERT: B 227 ASP cc_start: 0.8806 (m-30) cc_final: 0.8327 (p0) REVERT: C 34 LYS cc_start: 0.9329 (mmmt) cc_final: 0.8974 (mtpt) REVERT: C 121 LEU cc_start: 0.8893 (mp) cc_final: 0.8571 (pp) REVERT: C 137 ASN cc_start: 0.8976 (t0) cc_final: 0.8604 (t0) REVERT: C 307 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8904 (tppt) REVERT: D 24 GLU cc_start: 0.9338 (tp30) cc_final: 0.8946 (tp30) REVERT: D 153 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8568 (ttt-90) REVERT: E 56 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.7764 (p90) REVERT: E 102 ARG cc_start: 0.8317 (mtt-85) cc_final: 0.7578 (ttp-110) REVERT: E 103 TYR cc_start: 0.7948 (p90) cc_final: 0.7740 (p90) REVERT: E 105 ASN cc_start: 0.9111 (t0) cc_final: 0.8909 (t0) REVERT: E 131 ARG cc_start: 0.8494 (mtm110) cc_final: 0.8217 (mtm110) REVERT: E 262 ASN cc_start: 0.8785 (t0) cc_final: 0.8472 (t0) REVERT: F 92 VAL cc_start: 0.9274 (t) cc_final: 0.8967 (p) REVERT: F 140 LYS cc_start: 0.7578 (ptpt) cc_final: 0.6630 (tmmt) REVERT: F 142 ASN cc_start: 0.9305 (p0) cc_final: 0.8511 (p0) REVERT: F 172 GLU cc_start: 0.8522 (mm-30) cc_final: 0.7924 (mt-10) REVERT: G 41 MET cc_start: 0.9378 (tpt) cc_final: 0.9069 (mmm) REVERT: G 131 ARG cc_start: 0.8379 (ppt170) cc_final: 0.7995 (tmt170) REVERT: G 271 TYR cc_start: 0.7830 (t80) cc_final: 0.7487 (t80) REVERT: H 898 PHE cc_start: 0.7232 (t80) cc_final: 0.6888 (t80) REVERT: I 893 VAL cc_start: 0.8494 (t) cc_final: 0.8217 (p) REVERT: I 897 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7416 (tp30) REVERT: K 895 TYR cc_start: 0.8919 (m-80) cc_final: 0.8684 (m-80) REVERT: L 896 GLU cc_start: 0.8365 (tp30) cc_final: 0.8157 (tp30) outliers start: 49 outliers final: 26 residues processed: 179 average time/residue: 0.1496 time to fit residues: 41.5032 Evaluate side-chains 160 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain L residue 893 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 36 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 226 optimal weight: 8.9990 chunk 181 optimal weight: 3.9990 chunk 219 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 111 optimal weight: 0.6980 chunk 237 optimal weight: 50.0000 chunk 47 optimal weight: 0.0470 chunk 156 optimal weight: 4.9990 overall best weight: 2.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN D 203 HIS E 216 ASN G 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.079692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.054928 restraints weight = 56750.059| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.61 r_work: 0.2778 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20955 Z= 0.189 Angle : 0.549 8.140 28544 Z= 0.275 Chirality : 0.042 0.292 3197 Planarity : 0.004 0.051 3523 Dihedral : 13.257 115.506 3284 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.00 % Allowed : 14.99 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.18), residues: 2407 helix: 1.58 (0.14), residues: 1467 sheet: 0.01 (0.39), residues: 196 loop : 0.45 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 131 TYR 0.025 0.001 TYR G 110 PHE 0.015 0.001 PHE F 138 TRP 0.011 0.001 TRP F 284 HIS 0.004 0.001 HIS G 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (20955) covalent geometry : angle 0.54882 / 0.27 (28544) hydrogen bonds : bond 0.03970 / 2.61 ( 1078) hydrogen bonds : angle 3.71546 / 2.66 ( 2933) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 134 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8479 (p90) cc_final: 0.8142 (t80) REVERT: A 142 ASN cc_start: 0.8137 (m110) cc_final: 0.7686 (m110) REVERT: A 164 HIS cc_start: 0.8789 (t-90) cc_final: 0.8101 (t-90) REVERT: A 198 MET cc_start: 0.7957 (mtm) cc_final: 0.7439 (ptp) REVERT: A 328 GLN cc_start: 0.8318 (mt0) cc_final: 0.8067 (mp10) REVERT: B 73 LYS cc_start: 0.9074 (tptm) cc_final: 0.8631 (tppt) REVERT: B 137 ASN cc_start: 0.7854 (t0) cc_final: 0.7550 (p0) REVERT: B 220 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7647 (tp40) REVERT: B 227 ASP cc_start: 0.8843 (m-30) cc_final: 0.8384 (p0) REVERT: C 34 LYS cc_start: 0.9343 (mmmt) cc_final: 0.8994 (mtpt) REVERT: C 121 LEU cc_start: 0.8908 (mp) cc_final: 0.8610 (pp) REVERT: C 137 ASN cc_start: 0.8984 (t0) cc_final: 0.8588 (p0) REVERT: C 221 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8888 (mm) REVERT: D 24 GLU cc_start: 0.9363 (tp30) cc_final: 0.8969 (tp30) REVERT: D 142 ASN cc_start: 0.9074 (m-40) cc_final: 0.8168 (p0) REVERT: D 153 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8163 (ttt180) REVERT: D 291 ASP cc_start: 0.9395 (OUTLIER) cc_final: 0.9185 (t0) REVERT: E 56 TYR cc_start: 0.8654 (OUTLIER) cc_final: 0.7855 (p90) REVERT: E 210 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8594 (mp0) REVERT: E 262 ASN cc_start: 0.8795 (t0) cc_final: 0.8548 (t0) REVERT: F 92 VAL cc_start: 0.9263 (t) cc_final: 0.8958 (p) REVERT: F 140 LYS cc_start: 0.7564 (ptpt) cc_final: 0.6641 (tmmt) REVERT: F 142 ASN cc_start: 0.9312 (p0) cc_final: 0.8520 (p0) REVERT: F 172 GLU cc_start: 0.8619 (mm-30) cc_final: 0.7977 (mt-10) REVERT: G 68 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9216 (mm) REVERT: G 131 ARG cc_start: 0.8414 (ppt170) cc_final: 0.7994 (tmt170) REVERT: G 176 PHE cc_start: 0.7642 (OUTLIER) cc_final: 0.7346 (t80) REVERT: G 271 TYR cc_start: 0.7878 (t80) cc_final: 0.7563 (t80) REVERT: H 898 PHE cc_start: 0.7335 (t80) cc_final: 0.7101 (t80) REVERT: I 893 VAL cc_start: 0.8635 (t) cc_final: 0.8383 (p) REVERT: I 897 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7504 (tp30) REVERT: K 895 TYR cc_start: 0.8963 (m-80) cc_final: 0.8739 (m-80) outliers start: 63 outliers final: 33 residues processed: 186 average time/residue: 0.1459 time to fit residues: 42.5512 Evaluate side-chains 168 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain D residue 291 ASP Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 338 ASN Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 56 TYR Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 176 PHE Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 312 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 67 optimal weight: 7.9990 chunk 226 optimal weight: 8.9990 chunk 214 optimal weight: 0.0060 chunk 86 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 204 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 180 optimal weight: 0.0670 chunk 142 optimal weight: 0.0060 chunk 109 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 overall best weight: 0.7952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN C 197 ASN ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.080860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.056207 restraints weight = 55839.443| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.62 r_work: 0.2810 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20955 Z= 0.106 Angle : 0.496 9.947 28544 Z= 0.249 Chirality : 0.039 0.176 3197 Planarity : 0.003 0.048 3523 Dihedral : 13.092 112.063 3277 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.43 % Allowed : 15.80 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.18), residues: 2407 helix: 1.73 (0.14), residues: 1453 sheet: 0.03 (0.40), residues: 196 loop : 0.51 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 153 TYR 0.029 0.001 TYR G 110 PHE 0.014 0.001 PHE F 138 TRP 0.004 0.001 TRP F 284 HIS 0.004 0.001 HIS G 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (20955) covalent geometry : angle 0.49617 / 0.25 (28544) hydrogen bonds : bond 0.03656 / 2.42 ( 1078) hydrogen bonds : angle 3.55829 / 2.55 ( 2933) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 142 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8461 (p90) cc_final: 0.8152 (t80) REVERT: A 142 ASN cc_start: 0.8149 (m110) cc_final: 0.7702 (m110) REVERT: A 164 HIS cc_start: 0.8800 (t-90) cc_final: 0.8110 (t-90) REVERT: A 198 MET cc_start: 0.7939 (mtm) cc_final: 0.7414 (ptp) REVERT: A 221 LEU cc_start: 0.3609 (OUTLIER) cc_final: 0.3405 (mt) REVERT: B 73 LYS cc_start: 0.9055 (tptm) cc_final: 0.8617 (tppt) REVERT: B 137 ASN cc_start: 0.7849 (t0) cc_final: 0.7586 (p0) REVERT: B 172 GLU cc_start: 0.9233 (OUTLIER) cc_final: 0.8970 (mt-10) REVERT: B 184 LYS cc_start: 0.5892 (OUTLIER) cc_final: 0.5583 (tptm) REVERT: B 220 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7768 (tp40) REVERT: B 227 ASP cc_start: 0.8825 (m-30) cc_final: 0.8431 (p0) REVERT: C 34 LYS cc_start: 0.9330 (mmmt) cc_final: 0.8983 (mtpt) REVERT: C 121 LEU cc_start: 0.8876 (mp) cc_final: 0.8550 (pp) REVERT: C 137 ASN cc_start: 0.8969 (t0) cc_final: 0.8602 (t0) REVERT: C 221 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8848 (mm) REVERT: D 24 GLU cc_start: 0.9332 (tp30) cc_final: 0.8925 (tp30) REVERT: D 142 ASN cc_start: 0.9082 (m-40) cc_final: 0.8154 (p0) REVERT: D 166 ASP cc_start: 0.9380 (OUTLIER) cc_final: 0.9169 (m-30) REVERT: E 56 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.7749 (p90) REVERT: E 262 ASN cc_start: 0.8792 (t0) cc_final: 0.8511 (t0) REVERT: F 92 VAL cc_start: 0.9253 (t) cc_final: 0.8962 (p) REVERT: F 140 LYS cc_start: 0.7545 (ptpt) cc_final: 0.6605 (tmmt) REVERT: F 142 ASN cc_start: 0.9316 (p0) cc_final: 0.8522 (p0) REVERT: F 172 GLU cc_start: 0.8529 (mm-30) cc_final: 0.7852 (mt-10) REVERT: G 68 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9170 (mm) REVERT: G 110 TYR cc_start: 0.9150 (m-80) cc_final: 0.8947 (m-80) REVERT: G 131 ARG cc_start: 0.8427 (ppt170) cc_final: 0.8023 (tmt170) REVERT: G 271 TYR cc_start: 0.7835 (t80) cc_final: 0.7518 (t80) REVERT: H 898 PHE cc_start: 0.7300 (t80) cc_final: 0.7051 (t80) REVERT: I 893 VAL cc_start: 0.8689 (t) cc_final: 0.8464 (p) REVERT: I 897 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7470 (tp30) outliers start: 51 outliers final: 31 residues processed: 182 average time/residue: 0.1444 time to fit residues: 41.3081 Evaluate side-chains 166 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain L residue 893 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 23 optimal weight: 6.9990 chunk 208 optimal weight: 5.9990 chunk 141 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 203 optimal weight: 9.9990 chunk 158 optimal weight: 0.7980 chunk 154 optimal weight: 4.9990 chunk 214 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.079478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.054916 restraints weight = 56153.960| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.58 r_work: 0.2776 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20955 Z= 0.181 Angle : 0.530 9.624 28544 Z= 0.265 Chirality : 0.041 0.180 3197 Planarity : 0.004 0.046 3523 Dihedral : 13.132 111.862 3277 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.05 % Allowed : 15.80 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.18), residues: 2407 helix: 1.65 (0.14), residues: 1467 sheet: -0.02 (0.40), residues: 196 loop : 0.44 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 42 TYR 0.022 0.001 TYR G 110 PHE 0.013 0.001 PHE F 138 TRP 0.008 0.001 TRP F 284 HIS 0.004 0.001 HIS G 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (20955) covalent geometry : angle 0.53025 / 0.27 (28544) hydrogen bonds : bond 0.03779 / 2.50 ( 1078) hydrogen bonds : angle 3.60321 / 2.58 ( 2933) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 127 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8472 (p90) cc_final: 0.8165 (t80) REVERT: A 142 ASN cc_start: 0.8132 (m110) cc_final: 0.7685 (m110) REVERT: A 164 HIS cc_start: 0.8812 (t-90) cc_final: 0.8101 (t-90) REVERT: A 198 MET cc_start: 0.7950 (mtm) cc_final: 0.7439 (ptp) REVERT: A 215 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7496 (tpt90) REVERT: B 73 LYS cc_start: 0.9076 (tptm) cc_final: 0.8633 (tppt) REVERT: B 137 ASN cc_start: 0.7856 (t0) cc_final: 0.7599 (p0) REVERT: B 220 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7641 (tp40) REVERT: B 227 ASP cc_start: 0.8823 (m-30) cc_final: 0.8392 (p0) REVERT: C 34 LYS cc_start: 0.9331 (mmmt) cc_final: 0.9009 (mtpt) REVERT: C 121 LEU cc_start: 0.8893 (mp) cc_final: 0.8589 (pp) REVERT: C 137 ASN cc_start: 0.9005 (t0) cc_final: 0.8626 (p0) REVERT: C 221 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8878 (mm) REVERT: D 24 GLU cc_start: 0.9355 (tp30) cc_final: 0.8948 (tp30) REVERT: D 142 ASN cc_start: 0.9100 (m-40) cc_final: 0.8168 (p0) REVERT: D 166 ASP cc_start: 0.9375 (OUTLIER) cc_final: 0.9153 (m-30) REVERT: D 291 ASP cc_start: 0.9396 (OUTLIER) cc_final: 0.9179 (t0) REVERT: E 56 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.7846 (p90) REVERT: E 262 ASN cc_start: 0.8802 (t0) cc_final: 0.8581 (t0) REVERT: F 92 VAL cc_start: 0.9249 (t) cc_final: 0.8958 (p) REVERT: F 140 LYS cc_start: 0.7563 (ptpt) cc_final: 0.6605 (tmmt) REVERT: F 142 ASN cc_start: 0.9321 (p0) cc_final: 0.8544 (p0) REVERT: F 172 GLU cc_start: 0.8590 (mm-30) cc_final: 0.7911 (mt-10) REVERT: G 68 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9190 (mm) REVERT: G 110 TYR cc_start: 0.9183 (m-80) cc_final: 0.8933 (m-80) REVERT: G 131 ARG cc_start: 0.8452 (ppt170) cc_final: 0.8055 (tmt170) REVERT: G 176 PHE cc_start: 0.7627 (OUTLIER) cc_final: 0.7315 (t80) REVERT: G 271 TYR cc_start: 0.7865 (t80) cc_final: 0.7566 (t80) REVERT: H 898 PHE cc_start: 0.7382 (t80) cc_final: 0.7149 (t80) REVERT: I 893 VAL cc_start: 0.8768 (t) cc_final: 0.8545 (p) REVERT: I 897 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7482 (tp30) outliers start: 64 outliers final: 42 residues processed: 178 average time/residue: 0.1481 time to fit residues: 41.7954 Evaluate side-chains 176 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 126 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain D residue 291 ASP Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 338 ASN Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 56 TYR Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 176 PHE Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain L residue 893 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 144 optimal weight: 3.9990 chunk 224 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 192 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.080158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.055662 restraints weight = 56061.896| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 3.59 r_work: 0.2795 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20955 Z= 0.122 Angle : 0.510 10.222 28544 Z= 0.253 Chirality : 0.040 0.222 3197 Planarity : 0.003 0.048 3523 Dihedral : 13.051 108.298 3277 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.62 % Allowed : 16.18 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.18), residues: 2407 helix: 1.78 (0.14), residues: 1451 sheet: -0.02 (0.39), residues: 196 loop : 0.41 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 153 TYR 0.021 0.001 TYR G 110 PHE 0.013 0.001 PHE F 138 TRP 0.006 0.001 TRP F 284 HIS 0.004 0.001 HIS G 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (20955) covalent geometry : angle 0.51050 / 0.25 (28544) hydrogen bonds : bond 0.03594 / 2.38 ( 1078) hydrogen bonds : angle 3.51672 / 2.52 ( 2933) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 129 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8479 (p90) cc_final: 0.8172 (t80) REVERT: A 142 ASN cc_start: 0.8123 (m110) cc_final: 0.7689 (m110) REVERT: A 164 HIS cc_start: 0.8828 (t-90) cc_final: 0.8117 (t-90) REVERT: A 198 MET cc_start: 0.7887 (mtm) cc_final: 0.7363 (ptp) REVERT: A 215 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7470 (tpt90) REVERT: B 73 LYS cc_start: 0.9048 (tptm) cc_final: 0.8605 (tppt) REVERT: B 137 ASN cc_start: 0.7882 (t0) cc_final: 0.7639 (p0) REVERT: B 220 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7865 (tp40) REVERT: B 227 ASP cc_start: 0.8823 (m-30) cc_final: 0.8405 (p0) REVERT: C 34 LYS cc_start: 0.9328 (mmmt) cc_final: 0.8990 (mtpt) REVERT: C 121 LEU cc_start: 0.8885 (mp) cc_final: 0.8571 (pp) REVERT: C 137 ASN cc_start: 0.8962 (t0) cc_final: 0.8601 (t0) REVERT: C 221 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8843 (mm) REVERT: C 286 LYS cc_start: 0.9345 (OUTLIER) cc_final: 0.8448 (tptp) REVERT: D 24 GLU cc_start: 0.9347 (tp30) cc_final: 0.8936 (tp30) REVERT: D 142 ASN cc_start: 0.9080 (m-40) cc_final: 0.8174 (p0) REVERT: D 291 ASP cc_start: 0.9385 (OUTLIER) cc_final: 0.9180 (t0) REVERT: E 56 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.7749 (p90) REVERT: E 210 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8585 (mp0) REVERT: E 262 ASN cc_start: 0.8803 (t0) cc_final: 0.8572 (t0) REVERT: F 92 VAL cc_start: 0.9242 (t) cc_final: 0.8950 (p) REVERT: F 140 LYS cc_start: 0.7551 (ptpt) cc_final: 0.6579 (tmmt) REVERT: F 142 ASN cc_start: 0.9316 (p0) cc_final: 0.8546 (p0) REVERT: F 172 GLU cc_start: 0.8555 (mm-30) cc_final: 0.7867 (mt-10) REVERT: G 68 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9161 (mm) REVERT: G 110 TYR cc_start: 0.9146 (m-80) cc_final: 0.8907 (m-80) REVERT: G 131 ARG cc_start: 0.8455 (ppt170) cc_final: 0.8057 (tmt170) REVERT: G 176 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.7279 (t80) REVERT: H 898 PHE cc_start: 0.7357 (t80) cc_final: 0.7141 (t80) REVERT: I 893 VAL cc_start: 0.8825 (t) cc_final: 0.8592 (p) REVERT: I 897 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7523 (tp30) outliers start: 55 outliers final: 39 residues processed: 172 average time/residue: 0.1474 time to fit residues: 39.8317 Evaluate side-chains 170 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 123 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain D residue 291 ASP Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 338 ASN Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 176 PHE Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain L residue 893 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 157 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 223 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 chunk 48 optimal weight: 0.5980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.078946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.054403 restraints weight = 56625.299| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.58 r_work: 0.2740 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20955 Z= 0.179 Angle : 0.542 9.649 28544 Z= 0.268 Chirality : 0.041 0.167 3197 Planarity : 0.004 0.048 3523 Dihedral : 13.077 107.706 3277 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.05 % Allowed : 15.56 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.18), residues: 2407 helix: 1.76 (0.14), residues: 1452 sheet: -0.05 (0.40), residues: 196 loop : 0.40 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 153 TYR 0.018 0.001 TYR G 110 PHE 0.013 0.001 PHE B 23 TRP 0.009 0.001 TRP F 284 HIS 0.004 0.001 HIS G 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (20955) covalent geometry : angle 0.54237 / 0.27 (28544) hydrogen bonds : bond 0.03781 / 2.50 ( 1078) hydrogen bonds : angle 3.57675 / 2.57 ( 2933) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 128 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8503 (p90) cc_final: 0.8180 (t80) REVERT: A 142 ASN cc_start: 0.8125 (m110) cc_final: 0.7697 (m110) REVERT: A 164 HIS cc_start: 0.8840 (t-90) cc_final: 0.8127 (t-90) REVERT: A 198 MET cc_start: 0.7887 (mtm) cc_final: 0.7353 (ptp) REVERT: A 215 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7505 (tpt90) REVERT: B 73 LYS cc_start: 0.9063 (tptm) cc_final: 0.8608 (tppt) REVERT: B 137 ASN cc_start: 0.7881 (t0) cc_final: 0.7625 (p0) REVERT: B 220 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7599 (tp40) REVERT: B 227 ASP cc_start: 0.8803 (m-30) cc_final: 0.8415 (p0) REVERT: C 34 LYS cc_start: 0.9336 (mmmt) cc_final: 0.9019 (mtpt) REVERT: C 103 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.7982 (p90) REVERT: C 121 LEU cc_start: 0.8895 (mp) cc_final: 0.8604 (pp) REVERT: C 137 ASN cc_start: 0.8963 (t0) cc_final: 0.8616 (p0) REVERT: C 221 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8852 (mm) REVERT: D 142 ASN cc_start: 0.9104 (m-40) cc_final: 0.8200 (p0) REVERT: D 166 ASP cc_start: 0.9391 (OUTLIER) cc_final: 0.9175 (m-30) REVERT: E 56 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.7846 (p90) REVERT: F 92 VAL cc_start: 0.9235 (t) cc_final: 0.8934 (p) REVERT: F 140 LYS cc_start: 0.7563 (ptpt) cc_final: 0.6666 (tmmt) REVERT: F 142 ASN cc_start: 0.9311 (p0) cc_final: 0.8841 (p0) REVERT: F 172 GLU cc_start: 0.8594 (mm-30) cc_final: 0.7921 (mt-10) REVERT: G 68 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9181 (mm) REVERT: G 131 ARG cc_start: 0.8458 (ppt170) cc_final: 0.8083 (tmt170) REVERT: G 176 PHE cc_start: 0.7638 (OUTLIER) cc_final: 0.7285 (t80) REVERT: I 893 VAL cc_start: 0.8915 (t) cc_final: 0.8709 (p) REVERT: I 897 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7525 (tp30) outliers start: 64 outliers final: 44 residues processed: 177 average time/residue: 0.1421 time to fit residues: 39.7385 Evaluate side-chains 174 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 122 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 338 ASN Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 56 TYR Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 176 PHE Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain L residue 893 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 147 optimal weight: 0.3980 chunk 64 optimal weight: 0.9980 chunk 217 optimal weight: 0.5980 chunk 134 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 112 optimal weight: 0.4980 chunk 181 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.080022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.055554 restraints weight = 56211.415| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.58 r_work: 0.2768 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20955 Z= 0.109 Angle : 0.510 9.672 28544 Z= 0.252 Chirality : 0.039 0.150 3197 Planarity : 0.003 0.047 3523 Dihedral : 12.983 104.048 3277 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.14 % Allowed : 16.47 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.18), residues: 2407 helix: 1.80 (0.14), residues: 1452 sheet: -0.07 (0.39), residues: 196 loop : 0.41 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 153 TYR 0.022 0.001 TYR G 110 PHE 0.013 0.001 PHE F 138 TRP 0.005 0.001 TRP F 284 HIS 0.004 0.001 HIS G 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (20955) covalent geometry : angle 0.51032 / 0.25 (28544) hydrogen bonds : bond 0.03576 / 2.36 ( 1078) hydrogen bonds : angle 3.48198 / 2.50 ( 2933) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 131 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8485 (p90) cc_final: 0.8187 (t80) REVERT: A 142 ASN cc_start: 0.8154 (m110) cc_final: 0.7746 (m110) REVERT: A 164 HIS cc_start: 0.8849 (t-90) cc_final: 0.8142 (t-90) REVERT: A 198 MET cc_start: 0.7892 (mtm) cc_final: 0.7356 (ptp) REVERT: A 215 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7498 (tpt90) REVERT: B 73 LYS cc_start: 0.9053 (tptm) cc_final: 0.8606 (tppt) REVERT: B 137 ASN cc_start: 0.7867 (t0) cc_final: 0.7612 (p0) REVERT: B 220 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7843 (tp40) REVERT: B 227 ASP cc_start: 0.8767 (m-30) cc_final: 0.8464 (p0) REVERT: C 34 LYS cc_start: 0.9328 (mmmt) cc_final: 0.9011 (mtpt) REVERT: C 103 TYR cc_start: 0.8413 (p90) cc_final: 0.8019 (p90) REVERT: C 121 LEU cc_start: 0.8875 (mp) cc_final: 0.8571 (pp) REVERT: C 137 ASN cc_start: 0.8984 (t0) cc_final: 0.8634 (t0) REVERT: C 221 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8846 (mm) REVERT: D 142 ASN cc_start: 0.9100 (m-40) cc_final: 0.8227 (p0) REVERT: D 166 ASP cc_start: 0.9387 (OUTLIER) cc_final: 0.9174 (m-30) REVERT: E 56 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.7758 (p90) REVERT: E 105 ASN cc_start: 0.9021 (t0) cc_final: 0.8795 (t0) REVERT: F 92 VAL cc_start: 0.9233 (t) cc_final: 0.8947 (p) REVERT: F 140 LYS cc_start: 0.7557 (ptpt) cc_final: 0.6543 (tmmt) REVERT: F 142 ASN cc_start: 0.9313 (p0) cc_final: 0.8538 (p0) REVERT: F 172 GLU cc_start: 0.8558 (mm-30) cc_final: 0.7893 (mt-10) REVERT: G 41 MET cc_start: 0.9364 (tpp) cc_final: 0.9108 (tpp) REVERT: G 68 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9188 (mm) REVERT: G 131 ARG cc_start: 0.8466 (ppt170) cc_final: 0.8091 (tmt170) REVERT: I 897 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7545 (tp30) outliers start: 45 outliers final: 35 residues processed: 165 average time/residue: 0.1439 time to fit residues: 37.6250 Evaluate side-chains 167 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 126 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 338 ASN Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain I residue 896 GLU Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain L residue 893 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 19 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 67 optimal weight: 8.9990 chunk 173 optimal weight: 0.9990 chunk 218 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.079835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.055426 restraints weight = 56480.637| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.59 r_work: 0.2765 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20955 Z= 0.125 Angle : 0.517 12.777 28544 Z= 0.253 Chirality : 0.040 0.253 3197 Planarity : 0.003 0.046 3523 Dihedral : 12.960 103.639 3277 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.00 % Allowed : 16.94 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.18), residues: 2407 helix: 1.81 (0.14), residues: 1452 sheet: -0.08 (0.39), residues: 196 loop : 0.38 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 69 TYR 0.023 0.001 TYR G 110 PHE 0.013 0.001 PHE F 138 TRP 0.006 0.001 TRP F 284 HIS 0.004 0.001 HIS G 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (20955) covalent geometry : angle 0.51721 / 0.25 (28544) hydrogen bonds : bond 0.03558 / 2.35 ( 1078) hydrogen bonds : angle 3.48691 / 2.50 ( 2933) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4814 Ramachandran restraints generated. 2407 Oldfield, 0 Emsley, 2407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 125 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8486 (p90) cc_final: 0.8192 (t80) REVERT: A 142 ASN cc_start: 0.8158 (m110) cc_final: 0.7753 (m110) REVERT: A 164 HIS cc_start: 0.8853 (t-90) cc_final: 0.8151 (t-90) REVERT: A 198 MET cc_start: 0.7885 (mtm) cc_final: 0.7407 (ptp) REVERT: A 215 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7496 (tpt90) REVERT: B 73 LYS cc_start: 0.9047 (tptm) cc_final: 0.8604 (tppt) REVERT: B 137 ASN cc_start: 0.7882 (t0) cc_final: 0.7613 (p0) REVERT: B 220 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7892 (tp40) REVERT: B 227 ASP cc_start: 0.8757 (m-30) cc_final: 0.8458 (p0) REVERT: C 34 LYS cc_start: 0.9337 (mmmt) cc_final: 0.9017 (mtpt) REVERT: C 103 TYR cc_start: 0.8400 (p90) cc_final: 0.8010 (p90) REVERT: C 121 LEU cc_start: 0.8878 (mp) cc_final: 0.8575 (pp) REVERT: C 137 ASN cc_start: 0.8992 (t0) cc_final: 0.8648 (t0) REVERT: C 221 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8847 (mm) REVERT: D 142 ASN cc_start: 0.9098 (m-40) cc_final: 0.8236 (p0) REVERT: D 166 ASP cc_start: 0.9390 (OUTLIER) cc_final: 0.9174 (m-30) REVERT: E 56 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.7771 (p90) REVERT: E 94 ILE cc_start: 0.9031 (tp) cc_final: 0.8731 (pt) REVERT: E 105 ASN cc_start: 0.8978 (t0) cc_final: 0.8713 (t0) REVERT: F 92 VAL cc_start: 0.9233 (t) cc_final: 0.8956 (p) REVERT: F 140 LYS cc_start: 0.7571 (ptpt) cc_final: 0.6627 (tmmt) REVERT: F 142 ASN cc_start: 0.9313 (p0) cc_final: 0.8852 (p0) REVERT: F 172 GLU cc_start: 0.8593 (mm-30) cc_final: 0.7898 (mt-10) REVERT: G 68 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9194 (mm) REVERT: G 131 ARG cc_start: 0.8459 (ppt170) cc_final: 0.8102 (tmt170) REVERT: I 897 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7556 (tp30) outliers start: 42 outliers final: 35 residues processed: 157 average time/residue: 0.1444 time to fit residues: 35.5208 Evaluate side-chains 162 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 234 CYS Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 338 ASN Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain G residue 56 TYR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain L residue 893 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 38 optimal weight: 3.9990 chunk 178 optimal weight: 7.9990 chunk 114 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 235 optimal weight: 6.9990 chunk 204 optimal weight: 1.9990 chunk 196 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 220 GLN ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.079548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.055045 restraints weight = 56610.929| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.59 r_work: 0.2781 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20955 Z= 0.142 Angle : 0.524 13.651 28544 Z= 0.256 Chirality : 0.040 0.203 3197 Planarity : 0.003 0.046 3523 Dihedral : 12.939 101.265 3277 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.14 % Allowed : 16.75 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.18), residues: 2407 helix: 1.81 (0.14), residues: 1452 sheet: -0.10 (0.39), residues: 196 loop : 0.38 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 153 TYR 0.024 0.001 TYR G 110 PHE 0.013 0.001 PHE F 138 TRP 0.007 0.001 TRP F 284 HIS 0.004 0.001 HIS G 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (20955) covalent geometry : angle 0.52394 / 0.26 (28544) hydrogen bonds : bond 0.03598 / 2.38 ( 1078) hydrogen bonds : angle 3.49482 / 2.51 ( 2933) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4202.49 seconds wall clock time: 73 minutes 17.35 seconds (4397.35 seconds total)