Starting phenix.real_space_refine on Thu Sep 18 00:59:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ngs_49392/09_2025/9ngs_49392_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ngs_49392/09_2025/9ngs_49392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ngs_49392/09_2025/9ngs_49392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ngs_49392/09_2025/9ngs_49392.map" model { file = "/net/cci-nas-00/data/ceres_data/9ngs_49392/09_2025/9ngs_49392_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ngs_49392/09_2025/9ngs_49392_neut.cif" } resolution = 4.2 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 30 5.16 5 Na 4 4.78 5 C 8180 2.51 5 N 2085 2.21 5 O 2250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12549 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 8 Unusual residues: {' NA': 4, '3CN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Restraints were copied for chains: B, C, D, E Time building chain proxies: 2.25, per 1000 atoms: 0.18 Number of scatterers: 12549 At special positions: 0 Unit cell: (89.96, 89.96, 122.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 Na 4 11.00 O 2250 8.00 N 2085 7.00 C 8180 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: 1.29 Conformation dependent library (CDL) restraints added in 455.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 20 sheets defined 37.1% alpha, 41.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 62 through 70 removed outlier: 4.060A pdb=" N TRP A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 179 Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 208 through 221 Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 227 through 249 removed outlier: 4.148A pdb=" N ARG A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR A 241 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR A 249 " --> pdb=" O TYR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 260 through 286 Processing helix chain 'A' and resid 296 through 302 removed outlier: 3.910A pdb=" N ARG A 299 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N CYS A 300 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG A 301 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 302 " --> pdb=" O ARG A 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 296 through 302' Processing helix chain 'A' and resid 303 through 317 removed outlier: 3.708A pdb=" N ILE A 317 " --> pdb=" O CYS A 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 70 removed outlier: 4.060A pdb=" N TRP B 66 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 179 Processing helix chain 'B' and resid 201 through 208 Processing helix chain 'B' and resid 208 through 221 Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 227 through 249 removed outlier: 4.149A pdb=" N ARG B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR B 249 " --> pdb=" O TYR B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 252 No H-bonds generated for 'chain 'B' and resid 250 through 252' Processing helix chain 'B' and resid 260 through 286 Processing helix chain 'B' and resid 296 through 302 removed outlier: 3.911A pdb=" N ARG B 299 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N CYS B 300 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG B 301 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 302 " --> pdb=" O ARG B 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 296 through 302' Processing helix chain 'B' and resid 303 through 317 removed outlier: 3.708A pdb=" N ILE B 317 " --> pdb=" O CYS B 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 70 removed outlier: 4.059A pdb=" N TRP C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 179 Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 208 through 221 Processing helix chain 'C' and resid 222 through 225 Processing helix chain 'C' and resid 227 through 249 removed outlier: 4.148A pdb=" N ARG C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR C 241 " --> pdb=" O THR C 237 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR C 249 " --> pdb=" O TYR C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 252 No H-bonds generated for 'chain 'C' and resid 250 through 252' Processing helix chain 'C' and resid 260 through 286 Processing helix chain 'C' and resid 296 through 302 removed outlier: 3.910A pdb=" N ARG C 299 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N CYS C 300 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG C 301 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU C 302 " --> pdb=" O ARG C 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 296 through 302' Processing helix chain 'C' and resid 303 through 317 removed outlier: 3.708A pdb=" N ILE C 317 " --> pdb=" O CYS C 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 70 removed outlier: 4.060A pdb=" N TRP D 66 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 179 Processing helix chain 'D' and resid 201 through 208 Processing helix chain 'D' and resid 208 through 221 Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 227 through 249 removed outlier: 4.148A pdb=" N ARG D 231 " --> pdb=" O SER D 227 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR D 241 " --> pdb=" O THR D 237 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR D 249 " --> pdb=" O TYR D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 252 No H-bonds generated for 'chain 'D' and resid 250 through 252' Processing helix chain 'D' and resid 260 through 286 Processing helix chain 'D' and resid 296 through 302 removed outlier: 3.910A pdb=" N ARG D 299 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N CYS D 300 " --> pdb=" O ILE D 297 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG D 301 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU D 302 " --> pdb=" O ARG D 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 296 through 302' Processing helix chain 'D' and resid 303 through 317 removed outlier: 3.708A pdb=" N ILE D 317 " --> pdb=" O CYS D 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 70 removed outlier: 4.061A pdb=" N TRP E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 179 Processing helix chain 'E' and resid 201 through 208 Processing helix chain 'E' and resid 208 through 221 Processing helix chain 'E' and resid 222 through 225 Processing helix chain 'E' and resid 227 through 249 removed outlier: 4.148A pdb=" N ARG E 231 " --> pdb=" O SER E 227 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR E 241 " --> pdb=" O THR E 237 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR E 248 " --> pdb=" O ALA E 244 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR E 249 " --> pdb=" O TYR E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 252 No H-bonds generated for 'chain 'E' and resid 250 through 252' Processing helix chain 'E' and resid 260 through 286 Processing helix chain 'E' and resid 296 through 302 removed outlier: 3.910A pdb=" N ARG E 299 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N CYS E 300 " --> pdb=" O ILE E 297 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG E 301 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU E 302 " --> pdb=" O ARG E 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 296 through 302' Processing helix chain 'E' and resid 303 through 317 removed outlier: 3.708A pdb=" N ILE E 317 " --> pdb=" O CYS E 313 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 removed outlier: 4.238A pdb=" N SER A 109 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58 removed outlier: 3.512A pdb=" N GLY A 37 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY A 108 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR A 32 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLY A 25 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR A 44 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASP A 13 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL A 12 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER A 143 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL A 14 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE A 145 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A 16 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL A 147 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE A 18 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.417A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 198 " --> pdb=" O TRP A 161 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.417A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 58 removed outlier: 4.239A pdb=" N SER B 109 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 56 through 58 removed outlier: 3.512A pdb=" N GLY B 37 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY B 108 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR B 32 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLY B 25 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR B 44 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASP B 13 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL B 12 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N SER B 143 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N VAL B 14 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE B 145 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL B 16 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL B 147 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE B 18 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.417A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 198 " --> pdb=" O TRP B 161 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.417A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 56 through 58 removed outlier: 4.238A pdb=" N SER C 109 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 56 through 58 removed outlier: 3.512A pdb=" N GLY C 37 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY C 108 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR C 32 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLY C 25 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR C 44 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASP C 13 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL C 12 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER C 143 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL C 14 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE C 145 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL C 16 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL C 147 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE C 18 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.418A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C 198 " --> pdb=" O TRP C 161 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.418A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 56 through 58 removed outlier: 4.239A pdb=" N SER D 109 " --> pdb=" O VAL D 82 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 56 through 58 removed outlier: 3.511A pdb=" N GLY D 37 " --> pdb=" O PHE D 106 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY D 108 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR D 32 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLY D 25 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR D 44 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASP D 13 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL D 12 " --> pdb=" O ARG D 141 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER D 143 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL D 14 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE D 145 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL D 16 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL D 147 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE D 18 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.417A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL D 198 " --> pdb=" O TRP D 161 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.417A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 56 through 58 removed outlier: 4.239A pdb=" N SER E 109 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 56 through 58 removed outlier: 3.511A pdb=" N GLY E 37 " --> pdb=" O PHE E 106 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY E 108 " --> pdb=" O VAL E 35 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR E 32 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLY E 25 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR E 44 " --> pdb=" O ASP E 13 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASP E 13 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL E 12 " --> pdb=" O ARG E 141 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N SER E 143 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N VAL E 14 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE E 145 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL E 16 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL E 147 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE E 18 " --> pdb=" O VAL E 147 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.417A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL E 198 " --> pdb=" O TRP E 161 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.417A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) 665 hydrogen bonds defined for protein. 1905 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.26 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3966 1.34 - 1.46: 2473 1.46 - 1.57: 6391 1.57 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 12880 Sorted by residual: bond pdb=" C LEU B 210 " pdb=" N PRO B 211 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.28e-02 6.10e+03 1.62e+00 bond pdb=" C LEU D 210 " pdb=" N PRO D 211 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.28e-02 6.10e+03 1.61e+00 bond pdb=" C LEU C 210 " pdb=" N PRO C 211 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.28e-02 6.10e+03 1.57e+00 bond pdb=" C LEU A 210 " pdb=" N PRO A 211 " ideal model delta sigma weight residual 1.335 1.350 -0.016 1.28e-02 6.10e+03 1.54e+00 bond pdb=" CG LEU E 92 " pdb=" CD1 LEU E 92 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.53e+00 ... (remaining 12875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 16488 1.58 - 3.15: 823 3.15 - 4.73: 179 4.73 - 6.31: 30 6.31 - 7.89: 25 Bond angle restraints: 17545 Sorted by residual: angle pdb=" C ASN B 60 " pdb=" N THR B 61 " pdb=" CA THR B 61 " ideal model delta sigma weight residual 122.61 129.70 -7.09 1.56e+00 4.11e-01 2.07e+01 angle pdb=" C ASN D 60 " pdb=" N THR D 61 " pdb=" CA THR D 61 " ideal model delta sigma weight residual 122.61 129.63 -7.02 1.56e+00 4.11e-01 2.02e+01 angle pdb=" C ASN A 60 " pdb=" N THR A 61 " pdb=" CA THR A 61 " ideal model delta sigma weight residual 122.61 129.62 -7.01 1.56e+00 4.11e-01 2.02e+01 angle pdb=" C ASN E 60 " pdb=" N THR E 61 " pdb=" CA THR E 61 " ideal model delta sigma weight residual 122.61 129.59 -6.98 1.56e+00 4.11e-01 2.00e+01 angle pdb=" C ASN C 60 " pdb=" N THR C 61 " pdb=" CA THR C 61 " ideal model delta sigma weight residual 122.61 129.58 -6.97 1.56e+00 4.11e-01 2.00e+01 ... (remaining 17540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 6827 17.65 - 35.30: 568 35.30 - 52.95: 110 52.95 - 70.61: 15 70.61 - 88.26: 10 Dihedral angle restraints: 7530 sinusoidal: 3025 harmonic: 4505 Sorted by residual: dihedral pdb=" CA ARG B 190 " pdb=" C ARG B 190 " pdb=" N ILE B 191 " pdb=" CA ILE B 191 " ideal model delta harmonic sigma weight residual 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ARG D 190 " pdb=" C ARG D 190 " pdb=" N ILE D 191 " pdb=" CA ILE D 191 " ideal model delta harmonic sigma weight residual 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ARG A 190 " pdb=" C ARG A 190 " pdb=" N ILE A 191 " pdb=" CA ILE A 191 " ideal model delta harmonic sigma weight residual 180.00 160.06 19.94 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 7527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1156 0.040 - 0.080: 475 0.080 - 0.120: 233 0.120 - 0.160: 71 0.160 - 0.199: 15 Chirality restraints: 1950 Sorted by residual: chirality pdb=" CA THR C 61 " pdb=" N THR C 61 " pdb=" C THR C 61 " pdb=" CB THR C 61 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.95e-01 chirality pdb=" CA THR E 61 " pdb=" N THR E 61 " pdb=" C THR E 61 " pdb=" CB THR E 61 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" CA THR A 61 " pdb=" N THR A 61 " pdb=" C THR A 61 " pdb=" CB THR A 61 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.83e-01 ... (remaining 1947 not shown) Planarity restraints: 2235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 60 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.90e+00 pdb=" C ASN A 60 " 0.024 2.00e-02 2.50e+03 pdb=" O ASN A 60 " -0.009 2.00e-02 2.50e+03 pdb=" N THR A 61 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 60 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.90e+00 pdb=" C ASN B 60 " -0.024 2.00e-02 2.50e+03 pdb=" O ASN B 60 " 0.009 2.00e-02 2.50e+03 pdb=" N THR B 61 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 60 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.89e+00 pdb=" C ASN E 60 " 0.024 2.00e-02 2.50e+03 pdb=" O ASN E 60 " -0.009 2.00e-02 2.50e+03 pdb=" N THR E 61 " -0.008 2.00e-02 2.50e+03 ... (remaining 2232 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3617 2.82 - 3.34: 10972 3.34 - 3.86: 20240 3.86 - 4.38: 22357 4.38 - 4.90: 40355 Nonbonded interactions: 97541 Sorted by model distance: nonbonded pdb=" NH2 ARG D 255 " pdb=" CD1 ILE E 252 " model vdw 2.305 3.540 nonbonded pdb=" OE2 GLU D 131 " pdb=" ND 3CN D 401 " model vdw 2.312 3.120 nonbonded pdb=" OE2 GLU C 131 " pdb=" ND 3CN C 401 " model vdw 2.313 3.120 nonbonded pdb=" OE2 GLU E 131 " pdb=" ND 3CN E 401 " model vdw 2.314 3.120 nonbonded pdb=" OE2 GLU A 131 " pdb=" ND 3CN A 401 " model vdw 2.314 3.120 ... (remaining 97536 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 11 through 401) selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.260 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 12880 Z= 0.244 Angle : 0.865 7.887 17545 Z= 0.461 Chirality : 0.056 0.199 1950 Planarity : 0.005 0.034 2235 Dihedral : 13.906 88.257 4620 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.21), residues: 1525 helix: -0.56 (0.21), residues: 510 sheet: 0.48 (0.25), residues: 475 loop : -2.40 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 91 TYR 0.020 0.002 TYR B 245 PHE 0.021 0.002 PHE B 95 TRP 0.021 0.003 TRP C 72 HIS 0.004 0.001 HIS C 284 Details of bonding type rmsd covalent geometry : bond 0.00564 (12880) covalent geometry : angle 0.86506 (17545) hydrogen bonds : bond 0.17386 ( 575) hydrogen bonds : angle 7.97468 ( 1905) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 GLN cc_start: 0.7288 (mm-40) cc_final: 0.7025 (mm-40) REVERT: A 185 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7716 (mm-40) REVERT: A 265 MET cc_start: 0.8508 (ttp) cc_final: 0.8287 (ttt) REVERT: B 185 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7749 (mm-40) REVERT: C 138 GLN cc_start: 0.7014 (mm-40) cc_final: 0.6782 (mm-40) REVERT: C 185 GLN cc_start: 0.8260 (mm-40) cc_final: 0.7840 (mm-40) REVERT: C 282 PHE cc_start: 0.7158 (t80) cc_final: 0.6740 (t80) REVERT: D 138 GLN cc_start: 0.7034 (mm-40) cc_final: 0.6772 (mm-40) REVERT: D 185 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7776 (mm-40) REVERT: D 265 MET cc_start: 0.8521 (ttp) cc_final: 0.8300 (ttt) REVERT: D 282 PHE cc_start: 0.7197 (t80) cc_final: 0.6670 (t80) REVERT: E 62 GLN cc_start: 0.7206 (tm-30) cc_final: 0.6718 (tm-30) REVERT: E 138 GLN cc_start: 0.7068 (mm-40) cc_final: 0.6782 (mm-40) REVERT: E 185 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7758 (mm-40) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.0967 time to fit residues: 44.2990 Evaluate side-chains 244 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.0010 chunk 66 optimal weight: 0.0370 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 overall best weight: 0.5066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN B 124 GLN C 124 GLN D 124 GLN E 124 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.154542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.135906 restraints weight = 15934.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.136554 restraints weight = 12201.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.137882 restraints weight = 10205.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.138305 restraints weight = 8765.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.138534 restraints weight = 7827.728| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12880 Z= 0.105 Angle : 0.525 5.274 17545 Z= 0.272 Chirality : 0.046 0.134 1950 Planarity : 0.003 0.025 2235 Dihedral : 4.532 19.906 1690 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % 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 aren not related in a simple way. whole: -0.39 (0.22), residues: 1525 helix: 0.76 (0.23), residues: 505 sheet: 0.77 (0.25), residues: 470 loop : -2.21 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 190 TYR 0.009 0.001 TYR C 245 PHE 0.015 0.001 PHE E 95 TRP 0.018 0.001 TRP A 206 HIS 0.001 0.000 HIS E 284 Details of bonding type rmsd covalent geometry : bond 0.00224 (12880) covalent geometry : angle 0.52488 (17545) hydrogen bonds : bond 0.03415 ( 575) hydrogen bonds : angle 5.06115 ( 1905) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.7180 (tm-30) cc_final: 0.6869 (tm-30) REVERT: A 65 ARG cc_start: 0.7384 (ttp-170) cc_final: 0.7051 (ttp-170) REVERT: A 185 GLN cc_start: 0.7987 (mm-40) cc_final: 0.7705 (mm-40) REVERT: A 239 MET cc_start: 0.7318 (ttp) cc_final: 0.7002 (ttp) REVERT: B 252 ILE cc_start: 0.7944 (tp) cc_final: 0.7705 (tt) REVERT: B 263 ASP cc_start: 0.6937 (m-30) cc_final: 0.6729 (m-30) REVERT: C 138 GLN cc_start: 0.7217 (mm-40) cc_final: 0.6964 (mm-40) REVERT: C 252 ILE cc_start: 0.7855 (tp) cc_final: 0.7624 (tt) REVERT: D 79 ILE cc_start: 0.8771 (mm) cc_final: 0.8525 (mm) REVERT: D 259 THR cc_start: 0.7434 (p) cc_final: 0.7206 (p) REVERT: D 263 ASP cc_start: 0.6920 (m-30) cc_final: 0.6528 (m-30) REVERT: D 282 PHE cc_start: 0.7016 (t80) cc_final: 0.6476 (t80) REVERT: E 79 ILE cc_start: 0.8866 (mm) cc_final: 0.8642 (mm) REVERT: E 239 MET cc_start: 0.6999 (ttp) cc_final: 0.6750 (ttp) REVERT: E 252 ILE cc_start: 0.7893 (tp) cc_final: 0.7590 (tt) REVERT: E 259 THR cc_start: 0.7114 (p) cc_final: 0.6901 (p) REVERT: E 263 ASP cc_start: 0.7136 (m-30) cc_final: 0.6865 (m-30) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.0979 time to fit residues: 50.2208 Evaluate side-chains 280 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 7 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 GLN A 169 HIS ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN B 169 HIS ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN C 169 HIS ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 HIS ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 GLN E 169 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.145960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.126351 restraints weight = 16382.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.125756 restraints weight = 12770.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.127060 restraints weight = 12789.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.128137 restraints weight = 9924.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.131087 restraints weight = 8399.090| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 12880 Z= 0.233 Angle : 0.642 9.661 17545 Z= 0.334 Chirality : 0.050 0.188 1950 Planarity : 0.003 0.027 2235 Dihedral : 4.961 28.084 1690 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % 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 aren not related in a simple way. whole: -0.24 (0.22), residues: 1525 helix: 1.01 (0.23), residues: 510 sheet: 0.67 (0.26), residues: 465 loop : -2.07 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 65 TYR 0.027 0.002 TYR B 248 PHE 0.019 0.002 PHE E 95 TRP 0.021 0.002 TRP A 72 HIS 0.005 0.001 HIS E 177 Details of bonding type rmsd covalent geometry : bond 0.00556 (12880) covalent geometry : angle 0.64204 (17545) hydrogen bonds : bond 0.04003 ( 575) hydrogen bonds : angle 5.03274 ( 1905) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLN cc_start: 0.8028 (mt0) cc_final: 0.7177 (tp40) REVERT: A 239 MET cc_start: 0.7272 (ttp) cc_final: 0.7046 (ttp) REVERT: A 265 MET cc_start: 0.8349 (ttm) cc_final: 0.8062 (ttt) REVERT: B 62 GLN cc_start: 0.7317 (tm-30) cc_final: 0.6964 (tm-30) REVERT: B 139 GLN cc_start: 0.7968 (mt0) cc_final: 0.6917 (mm-40) REVERT: B 185 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7821 (mm-40) REVERT: B 259 THR cc_start: 0.7518 (p) cc_final: 0.7293 (p) REVERT: C 139 GLN cc_start: 0.8090 (mt0) cc_final: 0.7515 (tp40) REVERT: D 139 GLN cc_start: 0.7931 (mt0) cc_final: 0.7267 (tp40) REVERT: D 282 PHE cc_start: 0.7086 (t80) cc_final: 0.6449 (t80) REVERT: E 139 GLN cc_start: 0.7903 (mt0) cc_final: 0.7388 (tp40) REVERT: E 239 MET cc_start: 0.7248 (ttp) cc_final: 0.7007 (ttp) REVERT: E 259 THR cc_start: 0.7517 (p) cc_final: 0.7294 (p) outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.1102 time to fit residues: 51.1405 Evaluate side-chains 254 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 117 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 144 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN ** E 103 ASN ** 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 = 0.3462 r_free = 0.3462 target = 0.147676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.128327 restraints weight = 16130.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.128194 restraints weight = 12598.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.129251 restraints weight = 12562.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.130360 restraints weight = 9760.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.130550 restraints weight = 8479.437| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12880 Z= 0.157 Angle : 0.559 6.046 17545 Z= 0.288 Chirality : 0.048 0.134 1950 Planarity : 0.003 0.027 2235 Dihedral : 4.595 20.048 1690 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % 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 aren not related in a simple way. whole: -0.17 (0.22), residues: 1525 helix: 1.29 (0.24), residues: 505 sheet: 0.50 (0.26), residues: 460 loop : -2.01 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 255 TYR 0.020 0.001 TYR D 248 PHE 0.014 0.001 PHE E 95 TRP 0.021 0.002 TRP A 72 HIS 0.002 0.001 HIS E 177 Details of bonding type rmsd covalent geometry : bond 0.00366 (12880) covalent geometry : angle 0.55895 (17545) hydrogen bonds : bond 0.03405 ( 575) hydrogen bonds : angle 4.75252 ( 1905) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 ASN cc_start: 0.8028 (p0) cc_final: 0.7782 (p0) REVERT: A 139 GLN cc_start: 0.8031 (mt0) cc_final: 0.7101 (tp40) REVERT: A 204 TYR cc_start: 0.8131 (m-80) cc_final: 0.7815 (m-80) REVERT: A 265 MET cc_start: 0.8298 (ttm) cc_final: 0.8078 (ttt) REVERT: B 62 GLN cc_start: 0.7392 (tm-30) cc_final: 0.7083 (tm-30) REVERT: B 185 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7714 (mm-40) REVERT: B 239 MET cc_start: 0.7255 (ttp) cc_final: 0.6854 (ttp) REVERT: B 252 ILE cc_start: 0.7982 (tp) cc_final: 0.7649 (tt) REVERT: C 139 GLN cc_start: 0.7917 (mt0) cc_final: 0.7396 (tp40) REVERT: C 282 PHE cc_start: 0.7283 (t80) cc_final: 0.6927 (t80) REVERT: D 79 ILE cc_start: 0.8731 (mm) cc_final: 0.8520 (mm) REVERT: D 239 MET cc_start: 0.7227 (ttp) cc_final: 0.6967 (ttp) REVERT: D 252 ILE cc_start: 0.7967 (tp) cc_final: 0.7575 (tt) REVERT: D 259 THR cc_start: 0.7656 (p) cc_final: 0.7408 (p) REVERT: D 265 MET cc_start: 0.8411 (ttm) cc_final: 0.8162 (ttt) REVERT: D 279 LEU cc_start: 0.7995 (tt) cc_final: 0.7793 (tt) REVERT: D 282 PHE cc_start: 0.7136 (t80) cc_final: 0.6428 (t80) REVERT: E 79 ILE cc_start: 0.8781 (mm) cc_final: 0.8556 (mm) REVERT: E 139 GLN cc_start: 0.7782 (mt0) cc_final: 0.7225 (tp40) REVERT: E 239 MET cc_start: 0.7175 (ttp) cc_final: 0.6925 (ttp) REVERT: E 252 ILE cc_start: 0.8070 (tp) cc_final: 0.7819 (tt) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.0951 time to fit residues: 43.9535 Evaluate side-chains 259 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 138 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 133 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 ASN ** 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 = 0.3442 r_free = 0.3442 target = 0.145862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.128298 restraints weight = 16355.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.126770 restraints weight = 21693.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.127439 restraints weight = 19335.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.127600 restraints weight = 14331.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.128403 restraints weight = 11523.598| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12880 Z= 0.214 Angle : 0.630 9.092 17545 Z= 0.323 Chirality : 0.050 0.132 1950 Planarity : 0.003 0.027 2235 Dihedral : 4.869 29.289 1690 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.22), residues: 1525 helix: 1.11 (0.23), residues: 510 sheet: 0.34 (0.26), residues: 460 loop : -1.86 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 255 TYR 0.024 0.002 TYR E 248 PHE 0.013 0.002 PHE C 247 TRP 0.023 0.002 TRP A 72 HIS 0.003 0.001 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00507 (12880) covalent geometry : angle 0.62952 (17545) hydrogen bonds : bond 0.03778 ( 575) hydrogen bonds : angle 4.87293 ( 1905) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 THR cc_start: 0.8244 (m) cc_final: 0.7988 (p) REVERT: A 136 ASN cc_start: 0.8141 (p0) cc_final: 0.7847 (p0) REVERT: A 139 GLN cc_start: 0.8123 (mt0) cc_final: 0.7046 (tp40) REVERT: A 204 TYR cc_start: 0.8009 (m-80) cc_final: 0.7684 (m-80) REVERT: B 62 GLN cc_start: 0.7354 (tm-30) cc_final: 0.7111 (tm-30) REVERT: B 185 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7776 (mm-40) REVERT: B 239 MET cc_start: 0.7312 (ttp) cc_final: 0.6934 (ttp) REVERT: B 249 THR cc_start: 0.8046 (p) cc_final: 0.7843 (p) REVERT: B 252 ILE cc_start: 0.8011 (tp) cc_final: 0.7649 (tt) REVERT: C 139 GLN cc_start: 0.8067 (mt0) cc_final: 0.7074 (tp40) REVERT: C 282 PHE cc_start: 0.7180 (t80) cc_final: 0.6886 (t80) REVERT: D 239 MET cc_start: 0.7237 (ttp) cc_final: 0.6867 (ttp) REVERT: D 252 ILE cc_start: 0.8056 (tp) cc_final: 0.7624 (tt) REVERT: D 265 MET cc_start: 0.8461 (ttm) cc_final: 0.8238 (ttt) REVERT: D 282 PHE cc_start: 0.7199 (t80) cc_final: 0.6536 (t80) REVERT: E 239 MET cc_start: 0.7253 (ttp) cc_final: 0.7033 (ttp) REVERT: E 279 LEU cc_start: 0.7934 (tt) cc_final: 0.7734 (tp) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.0991 time to fit residues: 41.6719 Evaluate side-chains 246 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 5 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 62 optimal weight: 0.4980 chunk 119 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 146 optimal weight: 7.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 ASN C 103 ASN ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 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 = 0.3444 r_free = 0.3444 target = 0.145714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.125574 restraints weight = 16276.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.126133 restraints weight = 12482.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.127502 restraints weight = 10437.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.127710 restraints weight = 9278.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.127782 restraints weight = 8349.279| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12880 Z= 0.198 Angle : 0.608 7.503 17545 Z= 0.313 Chirality : 0.049 0.147 1950 Planarity : 0.003 0.029 2235 Dihedral : 4.854 27.585 1690 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % 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 aren not related in a simple way. whole: -0.30 (0.22), residues: 1525 helix: 1.10 (0.23), residues: 510 sheet: 0.28 (0.26), residues: 455 loop : -1.84 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 91 TYR 0.011 0.001 TYR E 248 PHE 0.011 0.001 PHE E 121 TRP 0.028 0.002 TRP B 220 HIS 0.003 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00471 (12880) covalent geometry : angle 0.60770 (17545) hydrogen bonds : bond 0.03643 ( 575) hydrogen bonds : angle 4.87168 ( 1905) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 THR cc_start: 0.8274 (m) cc_final: 0.8041 (p) REVERT: A 127 VAL cc_start: 0.9060 (t) cc_final: 0.8574 (p) REVERT: A 136 ASN cc_start: 0.8106 (p0) cc_final: 0.7800 (p0) REVERT: A 139 GLN cc_start: 0.8110 (mt0) cc_final: 0.6888 (tp40) REVERT: A 259 THR cc_start: 0.7481 (p) cc_final: 0.7245 (p) REVERT: A 265 MET cc_start: 0.8412 (ttt) cc_final: 0.8009 (ttp) REVERT: B 32 THR cc_start: 0.8646 (p) cc_final: 0.8432 (p) REVERT: B 239 MET cc_start: 0.7389 (ttp) cc_final: 0.6997 (ttp) REVERT: B 252 ILE cc_start: 0.7989 (tp) cc_final: 0.7744 (tt) REVERT: C 127 VAL cc_start: 0.8987 (t) cc_final: 0.8569 (p) REVERT: C 282 PHE cc_start: 0.7259 (t80) cc_final: 0.6919 (t80) REVERT: D 136 ASN cc_start: 0.8259 (p0) cc_final: 0.7953 (p0) REVERT: D 239 MET cc_start: 0.7271 (ttp) cc_final: 0.7024 (ttp) REVERT: D 252 ILE cc_start: 0.8030 (tp) cc_final: 0.7639 (tt) REVERT: E 136 ASN cc_start: 0.8113 (p0) cc_final: 0.7901 (p0) REVERT: E 239 MET cc_start: 0.7393 (ttp) cc_final: 0.7120 (ttp) REVERT: E 249 THR cc_start: 0.8120 (p) cc_final: 0.7725 (t) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.0923 time to fit residues: 37.7774 Evaluate side-chains 230 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 99 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 chunk 58 optimal weight: 0.0980 chunk 130 optimal weight: 3.9990 chunk 63 optimal weight: 0.0050 chunk 98 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 HIS ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 HIS ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 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 = 0.3499 r_free = 0.3499 target = 0.150941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.131580 restraints weight = 15961.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.131963 restraints weight = 12960.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.132750 restraints weight = 11975.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.134361 restraints weight = 9880.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.134204 restraints weight = 8102.004| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12880 Z= 0.108 Angle : 0.527 5.625 17545 Z= 0.271 Chirality : 0.047 0.144 1950 Planarity : 0.003 0.030 2235 Dihedral : 4.380 18.225 1690 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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 aren not related in a simple way. whole: -0.05 (0.22), residues: 1525 helix: 1.32 (0.24), residues: 510 sheet: 0.42 (0.26), residues: 455 loop : -1.71 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 190 TYR 0.014 0.001 TYR E 248 PHE 0.012 0.001 PHE D 282 TRP 0.033 0.002 TRP B 220 HIS 0.001 0.000 HIS E 284 Details of bonding type rmsd covalent geometry : bond 0.00242 (12880) covalent geometry : angle 0.52663 (17545) hydrogen bonds : bond 0.03100 ( 575) hydrogen bonds : angle 4.55267 ( 1905) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.9100 (t) cc_final: 0.8781 (p) REVERT: A 139 GLN cc_start: 0.7881 (mt0) cc_final: 0.6484 (tp40) REVERT: B 239 MET cc_start: 0.7265 (ttp) cc_final: 0.6757 (ttp) REVERT: B 252 ILE cc_start: 0.7981 (tp) cc_final: 0.7552 (tt) REVERT: C 127 VAL cc_start: 0.9011 (t) cc_final: 0.8722 (p) REVERT: C 282 PHE cc_start: 0.7264 (t80) cc_final: 0.6879 (t80) REVERT: D 239 MET cc_start: 0.7146 (ttp) cc_final: 0.6775 (ttp) REVERT: D 279 LEU cc_start: 0.7968 (tt) cc_final: 0.7755 (tt) REVERT: E 44 THR cc_start: 0.8312 (m) cc_final: 0.7972 (p) REVERT: E 239 MET cc_start: 0.7170 (ttp) cc_final: 0.6455 (ttp) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.0954 time to fit residues: 40.1363 Evaluate side-chains 255 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 121 optimal weight: 4.9990 chunk 28 optimal weight: 0.0270 chunk 95 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 31 optimal weight: 0.0040 overall best weight: 0.6054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.152682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.133479 restraints weight = 15955.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.134186 restraints weight = 12870.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.134692 restraints weight = 11146.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.134692 restraints weight = 9552.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.134692 restraints weight = 9552.000| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12880 Z= 0.104 Angle : 0.522 5.513 17545 Z= 0.267 Chirality : 0.047 0.151 1950 Planarity : 0.003 0.029 2235 Dihedral : 4.219 18.388 1690 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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 aren not related in a simple way. whole: 0.15 (0.22), residues: 1525 helix: 1.45 (0.23), residues: 510 sheet: 0.62 (0.27), residues: 455 loop : -1.66 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 190 TYR 0.014 0.001 TYR C 245 PHE 0.018 0.001 PHE D 304 TRP 0.037 0.002 TRP B 220 HIS 0.002 0.000 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00231 (12880) covalent geometry : angle 0.52186 (17545) hydrogen bonds : bond 0.02964 ( 575) hydrogen bonds : angle 4.38251 ( 1905) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.9151 (t) cc_final: 0.8828 (p) REVERT: A 139 GLN cc_start: 0.7827 (mt0) cc_final: 0.6760 (tp40) REVERT: A 249 THR cc_start: 0.7687 (p) cc_final: 0.7470 (p) REVERT: A 259 THR cc_start: 0.7448 (p) cc_final: 0.7162 (p) REVERT: A 265 MET cc_start: 0.8275 (ttm) cc_final: 0.8017 (ttt) REVERT: B 239 MET cc_start: 0.7324 (ttp) cc_final: 0.6589 (ttp) REVERT: B 249 THR cc_start: 0.7344 (p) cc_final: 0.7096 (p) REVERT: C 127 VAL cc_start: 0.9030 (t) cc_final: 0.8753 (p) REVERT: C 259 THR cc_start: 0.7328 (p) cc_final: 0.7103 (p) REVERT: C 282 PHE cc_start: 0.7164 (t80) cc_final: 0.6796 (t80) REVERT: D 239 MET cc_start: 0.7062 (ttp) cc_final: 0.6815 (ttp) REVERT: D 252 ILE cc_start: 0.7723 (tp) cc_final: 0.7454 (tt) REVERT: D 259 THR cc_start: 0.7383 (p) cc_final: 0.7080 (p) REVERT: E 44 THR cc_start: 0.8301 (m) cc_final: 0.7937 (p) REVERT: E 239 MET cc_start: 0.7029 (ttp) cc_final: 0.6507 (ttp) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.0932 time to fit residues: 39.8228 Evaluate side-chains 260 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 7.9990 chunk 145 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 110 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 146 optimal weight: 2.9990 chunk 127 optimal weight: 0.0870 chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.153293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.135921 restraints weight = 16040.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.135211 restraints weight = 24055.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.136493 restraints weight = 18722.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.137117 restraints weight = 13680.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.138020 restraints weight = 10549.919| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12880 Z= 0.110 Angle : 0.532 5.920 17545 Z= 0.270 Chirality : 0.047 0.144 1950 Planarity : 0.003 0.027 2235 Dihedral : 4.233 19.375 1690 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.22), residues: 1525 helix: 1.50 (0.23), residues: 510 sheet: 0.68 (0.26), residues: 455 loop : -1.61 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 190 TYR 0.016 0.001 TYR D 203 PHE 0.015 0.001 PHE B 95 TRP 0.032 0.002 TRP B 220 HIS 0.001 0.000 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00250 (12880) covalent geometry : angle 0.53231 (17545) hydrogen bonds : bond 0.03010 ( 575) hydrogen bonds : angle 4.34139 ( 1905) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.9093 (t) cc_final: 0.8811 (p) REVERT: A 249 THR cc_start: 0.7597 (p) cc_final: 0.7371 (p) REVERT: A 259 THR cc_start: 0.7363 (p) cc_final: 0.7147 (p) REVERT: A 265 MET cc_start: 0.8211 (ttm) cc_final: 0.7990 (ttp) REVERT: B 249 THR cc_start: 0.7106 (p) cc_final: 0.6839 (p) REVERT: C 127 VAL cc_start: 0.8999 (t) cc_final: 0.8721 (p) REVERT: C 190 ARG cc_start: 0.8618 (tpp-160) cc_final: 0.8339 (tpp-160) REVERT: C 282 PHE cc_start: 0.6995 (t80) cc_final: 0.6740 (t80) REVERT: D 239 MET cc_start: 0.7116 (ttp) cc_final: 0.6851 (ttp) REVERT: D 259 THR cc_start: 0.7414 (p) cc_final: 0.7188 (p) REVERT: E 44 THR cc_start: 0.8242 (m) cc_final: 0.7890 (p) REVERT: E 79 ILE cc_start: 0.8593 (mm) cc_final: 0.8376 (mm) REVERT: E 239 MET cc_start: 0.7050 (ttp) cc_final: 0.6411 (ttp) REVERT: E 249 THR cc_start: 0.6979 (p) cc_final: 0.6776 (p) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.0989 time to fit residues: 41.9225 Evaluate side-chains 260 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 143 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 137 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 ASN ** E 103 ASN ** 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 = 0.3451 r_free = 0.3451 target = 0.146142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.126475 restraints weight = 16456.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.125972 restraints weight = 13046.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.126594 restraints weight = 13794.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.127225 restraints weight = 11143.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.127230 restraints weight = 9917.977| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12880 Z= 0.215 Angle : 0.643 8.030 17545 Z= 0.327 Chirality : 0.050 0.139 1950 Planarity : 0.003 0.031 2235 Dihedral : 4.887 29.839 1690 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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 aren not related in a simple way. whole: 0.24 (0.22), residues: 1525 helix: 1.67 (0.24), residues: 480 sheet: 0.28 (0.25), residues: 490 loop : -1.28 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 190 TYR 0.019 0.002 TYR B 203 PHE 0.020 0.002 PHE B 95 TRP 0.032 0.002 TRP B 220 HIS 0.002 0.001 HIS E 177 Details of bonding type rmsd covalent geometry : bond 0.00511 (12880) covalent geometry : angle 0.64269 (17545) hydrogen bonds : bond 0.03637 ( 575) hydrogen bonds : angle 4.66714 ( 1905) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 127 VAL cc_start: 0.8957 (t) cc_final: 0.8571 (p) REVERT: C 282 PHE cc_start: 0.7289 (t80) cc_final: 0.6862 (t80) REVERT: D 239 MET cc_start: 0.7347 (ttp) cc_final: 0.7120 (ttp) REVERT: D 252 ILE cc_start: 0.7984 (tp) cc_final: 0.7703 (tt) REVERT: E 239 MET cc_start: 0.7408 (ttp) cc_final: 0.7200 (ttp) REVERT: E 249 THR cc_start: 0.7512 (p) cc_final: 0.7162 (p) REVERT: E 252 ILE cc_start: 0.7848 (tp) cc_final: 0.7581 (tt) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.0873 time to fit residues: 36.0629 Evaluate side-chains 237 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 119 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 79 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 138 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.150882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.131038 restraints weight = 16110.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.133368 restraints weight = 12989.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.133762 restraints weight = 10152.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.133926 restraints weight = 9123.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.133926 restraints weight = 8074.115| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12880 Z= 0.118 Angle : 0.553 6.519 17545 Z= 0.282 Chirality : 0.048 0.143 1950 Planarity : 0.003 0.031 2235 Dihedral : 4.475 20.916 1690 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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 aren not related in a simple way. whole: 0.37 (0.23), residues: 1525 helix: 1.81 (0.24), residues: 480 sheet: 0.51 (0.26), residues: 460 loop : -1.31 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 190 TYR 0.020 0.001 TYR C 245 PHE 0.023 0.001 PHE B 95 TRP 0.039 0.002 TRP C 220 HIS 0.001 0.000 HIS A 177 Details of bonding type rmsd covalent geometry : bond 0.00272 (12880) covalent geometry : angle 0.55327 (17545) hydrogen bonds : bond 0.03098 ( 575) hydrogen bonds : angle 4.45070 ( 1905) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1812.75 seconds wall clock time: 32 minutes 11.67 seconds (1931.67 seconds total)