Starting phenix.real_space_refine on Wed Feb 4 19:38:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ngs_49392/02_2026/9ngs_49392_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ngs_49392/02_2026/9ngs_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_49392/02_2026/9ngs_49392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ngs_49392/02_2026/9ngs_49392.map" model { file = "/net/cci-nas-00/data/ceres_data/9ngs_49392/02_2026/9ngs_49392_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ngs_49392/02_2026/9ngs_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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12549 Number of models: 1 Model: "" Number of chains: 10 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: "B" 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: "C" 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: "D" 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: "E" 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} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.96, per 1000 atoms: 0.24 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: 0.93 Conformation dependent library (CDL) restraints added in 572.9 milliseconds 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: 0.51 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: 2.13 Time building geometry restraints manager: 1.28 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 12.310 Find NCS groups from input model: 0.250 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.160 ------------------------------------------------------------------------------- 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 are 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 : 0.402 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: 0.8113 (mm-40) cc_final: 0.7716 (mm-40) REVERT: A 265 MET cc_start: 0.8509 (ttp) cc_final: 0.8288 (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: 0.7777 (mm-40) REVERT: D 265 MET cc_start: 0.8520 (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: 0.7207 (tm-30) cc_final: 0.6718 (tm-30) REVERT: E 86 ASP cc_start: 0.8388 (t0) cc_final: 0.8188 (t0) REVERT: E 138 GLN cc_start: 0.7068 (mm-40) cc_final: 0.6782 (mm-40) REVERT: E 185 GLN cc_start: 0.8187 (mm-40) cc_final: 0.7758 (mm-40) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.0833 time to fit residues: 38.5888 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 : 0.492 ------------------------------------------------------------------------------- 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 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 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 = 0.3537 r_free = 0.3537 target = 0.154708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.135981 restraints weight = 15890.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.137101 restraints weight = 12098.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.137503 restraints weight = 10460.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.138782 restraints weight = 9398.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.138987 restraints weight = 7936.060| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12880 Z= 0.102 Angle : 0.523 5.208 17545 Z= 0.271 Chirality : 0.046 0.135 1950 Planarity : 0.003 0.025 2235 Dihedral : 4.499 18.722 1690 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.88 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 are not related in a simple way. whole: -0.38 (0.22), residues: 1525 helix: 0.78 (0.23), residues: 505 sheet: 0.76 (0.25), residues: 470 loop : -2.19 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 99 TYR 0.008 0.001 TYR E 245 PHE 0.015 0.001 PHE E 95 TRP 0.018 0.001 TRP B 72 HIS 0.001 0.000 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00220 (12880) covalent geometry : angle 0.52310 (17545) hydrogen bonds : bond 0.03396 ( 575) hydrogen bonds : angle 5.00438 ( 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 335 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.7187 (tm-30) cc_final: 0.6880 (tm-30) REVERT: A 185 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7747 (mm-40) REVERT: A 239 MET cc_start: 0.7290 (ttp) cc_final: 0.6960 (ttp) REVERT: B 252 ILE cc_start: 0.7972 (tp) cc_final: 0.7729 (tt) REVERT: C 138 GLN cc_start: 0.7183 (mm-40) cc_final: 0.6939 (mm-40) REVERT: C 252 ILE cc_start: 0.7902 (tp) cc_final: 0.7640 (tt) REVERT: C 282 PHE cc_start: 0.7165 (t80) cc_final: 0.6887 (t80) REVERT: D 79 ILE cc_start: 0.8749 (mm) cc_final: 0.8512 (mm) REVERT: D 259 THR cc_start: 0.7393 (p) cc_final: 0.7161 (p) REVERT: D 263 ASP cc_start: 0.6906 (m-30) cc_final: 0.6511 (m-30) REVERT: D 282 PHE cc_start: 0.7016 (t80) cc_final: 0.6474 (t80) REVERT: E 79 ILE cc_start: 0.8849 (mm) cc_final: 0.8625 (mm) REVERT: E 239 MET cc_start: 0.6985 (ttp) cc_final: 0.6743 (ttp) REVERT: E 259 THR cc_start: 0.7105 (p) cc_final: 0.6899 (p) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.0887 time to fit residues: 45.2381 Evaluate side-chains 279 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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: 1.9990 chunk 147 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 88 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN D 62 GLN ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.152226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.136255 restraints weight = 16017.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.135992 restraints weight = 21559.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.136743 restraints weight = 18342.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.136109 restraints weight = 11503.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.136846 restraints weight = 8563.538| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12880 Z= 0.131 Angle : 0.531 5.509 17545 Z= 0.274 Chirality : 0.047 0.131 1950 Planarity : 0.003 0.024 2235 Dihedral : 4.346 18.835 1690 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.07 % Allowed : 2.33 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.22), residues: 1525 helix: 1.25 (0.23), residues: 510 sheet: 0.91 (0.26), residues: 465 loop : -1.99 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 190 TYR 0.017 0.001 TYR B 248 PHE 0.019 0.001 PHE C 142 TRP 0.019 0.001 TRP A 72 HIS 0.002 0.001 HIS E 177 Details of bonding type rmsd covalent geometry : bond 0.00304 (12880) covalent geometry : angle 0.53104 (17545) hydrogen bonds : bond 0.03387 ( 575) hydrogen bonds : angle 4.70729 ( 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 314 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 313 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.7117 (ttp) cc_final: 0.6854 (ttp) REVERT: B 62 GLN cc_start: 0.7265 (tm-30) cc_final: 0.7033 (tm-30) REVERT: B 185 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7746 (mm-40) REVERT: B 259 THR cc_start: 0.7409 (p) cc_final: 0.7187 (p) REVERT: C 138 GLN cc_start: 0.7367 (mm-40) cc_final: 0.7001 (mm-40) REVERT: D 62 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.6849 (tm-30) REVERT: D 139 GLN cc_start: 0.7757 (mt0) cc_final: 0.7070 (tp40) REVERT: D 263 ASP cc_start: 0.7078 (m-30) cc_final: 0.6706 (m-30) REVERT: D 282 PHE cc_start: 0.6933 (t80) cc_final: 0.6413 (t80) REVERT: E 139 GLN cc_start: 0.7547 (mt0) cc_final: 0.6845 (mm110) REVERT: E 239 MET cc_start: 0.7074 (ttp) cc_final: 0.6474 (ttp) REVERT: E 252 ILE cc_start: 0.7915 (tp) cc_final: 0.7594 (tt) outliers start: 1 outliers final: 0 residues processed: 314 average time/residue: 0.0938 time to fit residues: 44.5742 Evaluate side-chains 283 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 282 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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: 9.9990 chunk 0 optimal weight: 10.0000 chunk 144 optimal weight: 0.5980 chunk 48 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 169 HIS ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN ** 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 = 0.3466 r_free = 0.3466 target = 0.147759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.130880 restraints weight = 16153.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.130333 restraints weight = 23400.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.131862 restraints weight = 18873.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.131307 restraints weight = 10502.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.131899 restraints weight = 8461.112| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12880 Z= 0.188 Angle : 0.580 7.122 17545 Z= 0.300 Chirality : 0.049 0.131 1950 Planarity : 0.003 0.051 2235 Dihedral : 4.575 23.415 1690 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.22), residues: 1525 helix: 1.30 (0.24), residues: 510 sheet: 0.87 (0.26), residues: 465 loop : -1.93 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 255 TYR 0.025 0.002 TYR D 248 PHE 0.015 0.001 PHE C 142 TRP 0.021 0.001 TRP A 72 HIS 0.003 0.001 HIS E 177 Details of bonding type rmsd covalent geometry : bond 0.00444 (12880) covalent geometry : angle 0.57954 (17545) hydrogen bonds : bond 0.03515 ( 575) hydrogen bonds : angle 4.65999 ( 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 305 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 GLN cc_start: 0.8100 (mt0) cc_final: 0.7139 (tp40) REVERT: A 239 MET cc_start: 0.7227 (ttp) cc_final: 0.6938 (ttp) REVERT: A 259 THR cc_start: 0.7573 (p) cc_final: 0.7339 (p) REVERT: B 62 GLN cc_start: 0.7323 (tm-30) cc_final: 0.7041 (tm-30) REVERT: B 136 ASN cc_start: 0.7950 (p0) cc_final: 0.7744 (p0) REVERT: B 185 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7514 (mm-40) REVERT: C 62 GLN cc_start: 0.7333 (tm-30) cc_final: 0.6422 (tm-30) REVERT: C 127 VAL cc_start: 0.8854 (t) cc_final: 0.8544 (p) REVERT: C 138 GLN cc_start: 0.7549 (mm-40) cc_final: 0.7240 (mm-40) REVERT: C 139 GLN cc_start: 0.7945 (mt0) cc_final: 0.7501 (tp40) REVERT: D 62 GLN cc_start: 0.7783 (tp-100) cc_final: 0.7415 (tp40) REVERT: D 139 GLN cc_start: 0.7943 (mt0) cc_final: 0.7362 (tp40) REVERT: D 239 MET cc_start: 0.7334 (ttp) cc_final: 0.7035 (ttp) REVERT: D 259 THR cc_start: 0.7638 (p) cc_final: 0.7389 (p) REVERT: D 282 PHE cc_start: 0.6943 (t80) cc_final: 0.6351 (t80) REVERT: E 79 ILE cc_start: 0.8786 (mm) cc_final: 0.8567 (mm) REVERT: E 139 GLN cc_start: 0.7873 (mt0) cc_final: 0.7326 (tp40) REVERT: E 239 MET cc_start: 0.7124 (ttp) cc_final: 0.6883 (ttp) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.0845 time to fit residues: 39.1432 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 : 0.453 ------------------------------------------------------------------------------- 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: 0.9990 chunk 49 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 133 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.148669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.128356 restraints weight = 16090.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.130885 restraints weight = 13312.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.131043 restraints weight = 10038.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.131056 restraints weight = 9037.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.131725 restraints weight = 8207.522| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12880 Z= 0.180 Angle : 0.582 6.985 17545 Z= 0.299 Chirality : 0.049 0.132 1950 Planarity : 0.003 0.037 2235 Dihedral : 4.547 20.744 1690 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.22), residues: 1525 helix: 1.35 (0.24), residues: 510 sheet: 0.64 (0.26), residues: 455 loop : -1.89 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 190 TYR 0.019 0.001 TYR B 248 PHE 0.010 0.001 PHE C 142 TRP 0.022 0.002 TRP A 72 HIS 0.003 0.001 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00426 (12880) covalent geometry : angle 0.58162 (17545) hydrogen bonds : bond 0.03510 ( 575) hydrogen bonds : angle 4.69178 ( 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 294 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 THR cc_start: 0.8232 (m) cc_final: 0.7981 (p) REVERT: A 139 GLN cc_start: 0.8016 (mt0) cc_final: 0.7007 (tp40) REVERT: A 239 MET cc_start: 0.7298 (ttp) cc_final: 0.6979 (ttp) REVERT: B 62 GLN cc_start: 0.7351 (tm-30) cc_final: 0.7071 (tm-30) REVERT: C 127 VAL cc_start: 0.8963 (t) cc_final: 0.8551 (p) REVERT: C 139 GLN cc_start: 0.7859 (mt0) cc_final: 0.7164 (tp40) REVERT: C 282 PHE cc_start: 0.7278 (t80) cc_final: 0.6912 (t80) REVERT: D 139 GLN cc_start: 0.7881 (mt0) cc_final: 0.7315 (tp40) REVERT: D 239 MET cc_start: 0.7272 (ttp) cc_final: 0.6950 (ttp) REVERT: D 259 THR cc_start: 0.7607 (p) cc_final: 0.7389 (p) REVERT: D 279 LEU cc_start: 0.7932 (tt) cc_final: 0.7727 (tt) REVERT: D 282 PHE cc_start: 0.7025 (t80) cc_final: 0.6352 (t80) REVERT: E 139 GLN cc_start: 0.7759 (mt0) cc_final: 0.7247 (tp40) REVERT: E 239 MET cc_start: 0.7211 (ttp) cc_final: 0.6930 (ttp) REVERT: E 259 THR cc_start: 0.7307 (p) cc_final: 0.7065 (p) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.0964 time to fit residues: 42.5575 Evaluate side-chains 245 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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: 5.9990 chunk 56 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 119 optimal weight: 0.1980 chunk 79 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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** ** 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 = 0.3476 r_free = 0.3476 target = 0.148843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.131624 restraints weight = 16127.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.130807 restraints weight = 24049.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.132114 restraints weight = 19748.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.131851 restraints weight = 11327.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.132406 restraints weight = 8956.369| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2323 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= 0.171 Angle : 0.582 7.208 17545 Z= 0.298 Chirality : 0.048 0.131 1950 Planarity : 0.003 0.055 2235 Dihedral : 4.585 20.858 1690 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.22), residues: 1525 helix: 1.26 (0.24), residues: 510 sheet: 0.48 (0.26), residues: 460 loop : -1.77 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 190 TYR 0.014 0.001 TYR A 203 PHE 0.010 0.001 PHE D 228 TRP 0.024 0.002 TRP A 72 HIS 0.003 0.001 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00402 (12880) covalent geometry : angle 0.58162 (17545) hydrogen bonds : bond 0.03446 ( 575) hydrogen bonds : angle 4.65290 ( 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 286 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 ASN cc_start: 0.7951 (p0) cc_final: 0.7732 (p0) REVERT: A 139 GLN cc_start: 0.8171 (mt0) cc_final: 0.7032 (tp40) REVERT: A 239 MET cc_start: 0.7210 (ttp) cc_final: 0.6969 (ttp) REVERT: B 62 GLN cc_start: 0.7372 (tm-30) cc_final: 0.7097 (tm-30) REVERT: B 185 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7878 (mm-40) REVERT: C 127 VAL cc_start: 0.8986 (t) cc_final: 0.8539 (p) REVERT: C 139 GLN cc_start: 0.7943 (mt0) cc_final: 0.7075 (tp40) REVERT: C 282 PHE cc_start: 0.7196 (t80) cc_final: 0.6911 (t80) REVERT: D 136 ASN cc_start: 0.8152 (p0) cc_final: 0.7893 (p0) REVERT: D 139 GLN cc_start: 0.8065 (mt0) cc_final: 0.7347 (tp40) REVERT: D 239 MET cc_start: 0.7248 (ttp) cc_final: 0.6994 (ttp) REVERT: D 282 PHE cc_start: 0.7021 (t80) cc_final: 0.6382 (t80) REVERT: E 79 ILE cc_start: 0.8708 (mm) cc_final: 0.8426 (mm) REVERT: E 139 GLN cc_start: 0.7814 (mt0) cc_final: 0.7118 (tp40) REVERT: E 239 MET cc_start: 0.7197 (ttp) cc_final: 0.6558 (ttp) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.0941 time to fit residues: 41.4532 Evaluate side-chains 243 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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: 6.9990 chunk 29 optimal weight: 0.5980 chunk 58 optimal weight: 20.0000 chunk 130 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** ** 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 = 0.3519 r_free = 0.3519 target = 0.152482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.132385 restraints weight = 15904.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.134149 restraints weight = 12535.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.134496 restraints weight = 10194.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.134997 restraints weight = 9548.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.134997 restraints weight = 8268.248| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12880 Z= 0.109 Angle : 0.529 6.758 17545 Z= 0.270 Chirality : 0.047 0.140 1950 Planarity : 0.003 0.029 2235 Dihedral : 4.266 14.905 1690 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.22), residues: 1525 helix: 1.40 (0.24), residues: 510 sheet: 0.63 (0.26), residues: 455 loop : -1.70 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 91 TYR 0.013 0.001 TYR E 248 PHE 0.016 0.001 PHE E 228 TRP 0.026 0.002 TRP B 220 HIS 0.002 0.000 HIS E 284 Details of bonding type rmsd covalent geometry : bond 0.00246 (12880) covalent geometry : angle 0.52891 (17545) hydrogen bonds : bond 0.03060 ( 575) hydrogen bonds : angle 4.44282 ( 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 282 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 GLN cc_start: 0.7838 (mt0) cc_final: 0.6802 (tp40) REVERT: A 190 ARG cc_start: 0.8514 (tpp-160) cc_final: 0.8179 (tpp-160) REVERT: A 239 MET cc_start: 0.7297 (ttp) cc_final: 0.6946 (ttp) REVERT: A 259 THR cc_start: 0.7274 (p) cc_final: 0.7069 (p) REVERT: B 127 VAL cc_start: 0.9050 (t) cc_final: 0.8698 (p) REVERT: C 127 VAL cc_start: 0.8965 (t) cc_final: 0.8637 (p) REVERT: C 139 GLN cc_start: 0.7697 (mt0) cc_final: 0.7294 (tp40) REVERT: C 204 TYR cc_start: 0.7800 (m-80) cc_final: 0.7224 (m-80) REVERT: C 259 THR cc_start: 0.7187 (p) cc_final: 0.6978 (p) REVERT: C 282 PHE cc_start: 0.7233 (t80) cc_final: 0.6874 (t80) REVERT: D 139 GLN cc_start: 0.7844 (mt0) cc_final: 0.7222 (tp40) REVERT: D 239 MET cc_start: 0.7089 (ttp) cc_final: 0.6484 (ttp) REVERT: D 279 LEU cc_start: 0.7967 (tt) cc_final: 0.7758 (tt) REVERT: D 282 PHE cc_start: 0.6975 (t80) cc_final: 0.6326 (t80) REVERT: E 44 THR cc_start: 0.8259 (m) cc_final: 0.7913 (p) REVERT: E 139 GLN cc_start: 0.7499 (mt0) cc_final: 0.6999 (tp40) REVERT: E 239 MET cc_start: 0.7047 (ttp) cc_final: 0.6382 (ttp) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.0921 time to fit residues: 39.4478 Evaluate side-chains 264 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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: 0.0060 chunk 28 optimal weight: 6.9990 chunk 95 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 89 optimal weight: 0.0980 chunk 31 optimal weight: 9.9990 overall best weight: 0.5400 ------------------------------------------------------------------------------- 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** ** 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 = 0.3543 r_free = 0.3543 target = 0.154999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.135664 restraints weight = 15828.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.137710 restraints weight = 11642.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.138446 restraints weight = 9174.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.140303 restraints weight = 7910.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.140288 restraints weight = 6454.056| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12880 Z= 0.099 Angle : 0.513 5.419 17545 Z= 0.261 Chirality : 0.046 0.135 1950 Planarity : 0.002 0.028 2235 Dihedral : 4.067 17.100 1690 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % 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 are not related in a simple way. whole: 0.30 (0.22), residues: 1525 helix: 1.51 (0.23), residues: 510 sheet: 0.67 (0.26), residues: 485 loop : -1.58 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 190 TYR 0.019 0.001 TYR D 203 PHE 0.013 0.001 PHE B 95 TRP 0.033 0.001 TRP B 220 HIS 0.002 0.000 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00217 (12880) covalent geometry : angle 0.51261 (17545) hydrogen bonds : bond 0.02905 ( 575) hydrogen bonds : angle 4.24323 ( 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 304 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.7209 (ttp) cc_final: 0.6793 (ttp) REVERT: B 127 VAL cc_start: 0.9065 (t) cc_final: 0.8793 (p) REVERT: C 127 VAL cc_start: 0.8996 (t) cc_final: 0.8703 (p) REVERT: C 282 PHE cc_start: 0.7197 (t80) cc_final: 0.6885 (t80) REVERT: D 279 LEU cc_start: 0.8038 (tt) cc_final: 0.7827 (tt) REVERT: D 282 PHE cc_start: 0.6880 (t80) cc_final: 0.6286 (t80) REVERT: E 190 ARG cc_start: 0.8402 (tpp-160) cc_final: 0.8115 (tpp-160) REVERT: E 239 MET cc_start: 0.6927 (ttp) cc_final: 0.6337 (ttp) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.0974 time to fit residues: 44.9013 Evaluate side-chains 268 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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: 0.0970 chunk 145 optimal weight: 0.9980 chunk 26 optimal weight: 10.0000 chunk 110 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- 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** ** 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 = 0.3518 r_free = 0.3518 target = 0.152210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.135491 restraints weight = 16045.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.134929 restraints weight = 22871.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.136153 restraints weight = 18699.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.136139 restraints weight = 14389.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.136661 restraints weight = 10665.757| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12880 Z= 0.137 Angle : 0.559 5.961 17545 Z= 0.283 Chirality : 0.047 0.138 1950 Planarity : 0.003 0.028 2235 Dihedral : 4.282 18.431 1690 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % 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 are not related in a simple way. whole: 0.32 (0.23), residues: 1525 helix: 1.57 (0.24), residues: 510 sheet: 0.65 (0.26), residues: 490 loop : -1.59 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 91 TYR 0.021 0.001 TYR B 248 PHE 0.015 0.001 PHE A 142 TRP 0.029 0.002 TRP B 220 HIS 0.001 0.000 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00319 (12880) covalent geometry : angle 0.55874 (17545) hydrogen bonds : bond 0.03142 ( 575) hydrogen bonds : angle 4.32985 ( 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 286 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.7719 (mp) cc_final: 0.7469 (mp) REVERT: A 140 LEU cc_start: 0.8576 (tt) cc_final: 0.8327 (tt) REVERT: A 239 MET cc_start: 0.7253 (ttp) cc_final: 0.6568 (ttp) REVERT: B 127 VAL cc_start: 0.9036 (t) cc_final: 0.8707 (p) REVERT: C 127 VAL cc_start: 0.8972 (t) cc_final: 0.8615 (p) REVERT: C 139 GLN cc_start: 0.7901 (mt0) cc_final: 0.7074 (tp40) REVERT: C 204 TYR cc_start: 0.7832 (m-80) cc_final: 0.7201 (m-80) REVERT: D 79 ILE cc_start: 0.8532 (mm) cc_final: 0.8308 (mm) REVERT: D 139 GLN cc_start: 0.7790 (mt0) cc_final: 0.7225 (tp40) REVERT: D 282 PHE cc_start: 0.6826 (t80) cc_final: 0.6279 (t80) REVERT: E 139 GLN cc_start: 0.7461 (mt0) cc_final: 0.7064 (tp40) REVERT: E 239 MET cc_start: 0.6932 (ttp) cc_final: 0.6133 (ttp) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.0946 time to fit residues: 41.1014 Evaluate side-chains 266 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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: 3.9990 chunk 48 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 chunk 137 optimal weight: 9.9990 chunk 123 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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** ** 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 = 0.3508 r_free = 0.3508 target = 0.151421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.135284 restraints weight = 16138.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.135044 restraints weight = 20635.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.135393 restraints weight = 18682.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.135225 restraints weight = 10541.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.135622 restraints weight = 8624.646| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12880 Z= 0.136 Angle : 0.556 6.333 17545 Z= 0.283 Chirality : 0.048 0.144 1950 Planarity : 0.003 0.029 2235 Dihedral : 4.398 19.765 1690 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % 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 are not related in a simple way. whole: 0.61 (0.23), residues: 1525 helix: 1.94 (0.24), residues: 480 sheet: 0.60 (0.26), residues: 490 loop : -1.17 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 91 TYR 0.015 0.001 TYR A 245 PHE 0.018 0.001 PHE D 142 TRP 0.028 0.002 TRP B 220 HIS 0.002 0.000 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00316 (12880) covalent geometry : angle 0.55560 (17545) hydrogen bonds : bond 0.03186 ( 575) hydrogen bonds : angle 4.38175 ( 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 288 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 259 THR cc_start: 0.7372 (p) cc_final: 0.7165 (p) REVERT: B 127 VAL cc_start: 0.9032 (t) cc_final: 0.8681 (p) REVERT: C 139 GLN cc_start: 0.7936 (mt0) cc_final: 0.7095 (tp40) REVERT: C 282 PHE cc_start: 0.7166 (t80) cc_final: 0.6839 (t80) REVERT: D 79 ILE cc_start: 0.8531 (mm) cc_final: 0.8293 (mm) REVERT: D 139 GLN cc_start: 0.7789 (mt0) cc_final: 0.7261 (tp40) REVERT: D 249 THR cc_start: 0.7352 (p) cc_final: 0.6998 (p) REVERT: D 252 ILE cc_start: 0.7552 (tp) cc_final: 0.7227 (tt) REVERT: D 265 MET cc_start: 0.8320 (ttm) cc_final: 0.8120 (ttm) REVERT: D 279 LEU cc_start: 0.8085 (tt) cc_final: 0.7877 (tt) REVERT: D 282 PHE cc_start: 0.6920 (t80) cc_final: 0.6328 (t80) REVERT: E 139 GLN cc_start: 0.7496 (mt0) cc_final: 0.7044 (tp40) REVERT: E 239 MET cc_start: 0.6876 (ttp) cc_final: 0.6496 (ttp) REVERT: E 249 THR cc_start: 0.7252 (p) cc_final: 0.6971 (p) REVERT: E 252 ILE cc_start: 0.7765 (tp) cc_final: 0.7536 (tt) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.0968 time to fit residues: 42.4694 Evaluate side-chains 266 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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: 1.9990 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 146 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 138 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 C 103 ASN ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.147813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.130092 restraints weight = 16218.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.129842 restraints weight = 23569.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.130658 restraints weight = 21629.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.131116 restraints weight = 15389.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.131247 restraints weight = 13717.550| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12880 Z= 0.194 Angle : 0.624 7.897 17545 Z= 0.319 Chirality : 0.050 0.170 1950 Planarity : 0.003 0.029 2235 Dihedral : 4.752 27.069 1690 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % 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 are not related in a simple way. whole: 0.37 (0.23), residues: 1525 helix: 1.78 (0.24), residues: 480 sheet: 0.38 (0.25), residues: 490 loop : -1.24 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 255 TYR 0.017 0.002 TYR C 245 PHE 0.024 0.002 PHE B 95 TRP 0.027 0.002 TRP B 220 HIS 0.003 0.001 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00461 (12880) covalent geometry : angle 0.62404 (17545) hydrogen bonds : bond 0.03570 ( 575) hydrogen bonds : angle 4.60142 ( 1905) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1720.02 seconds wall clock time: 30 minutes 32.57 seconds (1832.57 seconds total)