Starting phenix.real_space_refine on Fri Jul 3 01:30:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w1x_65558/07_2026/9w1x_65558.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w1x_65558/07_2026/9w1x_65558.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w1x_65558/07_2026/9w1x_65558.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w1x_65558/07_2026/9w1x_65558.map" model { file = "/net/cci-nas-00/data/ceres_data/9w1x_65558/07_2026/9w1x_65558.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w1x_65558/07_2026/9w1x_65558.cif" } resolution = 4.6 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= 0.006 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 6992 2.51 5 N 1916 2.21 5 O 2072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11064 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2766 Classifications: {'peptide': 346} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 329} Restraints were copied for chains: a, B, b Time building chain proxies: 2.12, per 1000 atoms: 0.19 Number of scatterers: 11064 At special positions: 0 Unit cell: (91.927, 123.464, 107.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2072 8.00 N 1916 7.00 C 6992 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 15 " distance=2.00 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS B 4 " distance=2.58 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS B 4 " distance=1.44 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS B 15 " distance=2.60 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 316 " distance=2.03 Simple disulfide: pdb=" SG CYS a 4 " - pdb=" SG CYS a 15 " distance=2.00 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 15 " distance=2.00 Simple disulfide: pdb=" SG CYS b 4 " - pdb=" SG CYS b 15 " distance=2.00 Simple disulfide: pdb=" SG CYS a 55 " - pdb=" SG CYS a 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS b 55 " - pdb=" SG CYS b 143 " distance=2.03 Simple disulfide: pdb=" SG CYS a 179 " - pdb=" SG CYS a 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS b 179 " - pdb=" SG CYS b 223 " distance=2.03 Simple disulfide: pdb=" SG CYS a 280 " - pdb=" SG CYS a 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS b 280 " - pdb=" SG CYS b 329 " distance=2.03 Simple disulfide: pdb=" SG CYS a 291 " - pdb=" SG CYS a 312 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 312 " distance=2.03 Simple disulfide: pdb=" SG CYS b 291 " - pdb=" SG CYS b 312 " distance=2.03 Simple disulfide: pdb=" SG CYS a 313 " - pdb=" SG CYS a 316 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 316 " distance=2.03 Simple disulfide: pdb=" SG CYS b 313 " - pdb=" SG CYS b 316 " distance=2.03 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: 0.82 Conformation dependent library (CDL) restraints added in 382.5 milliseconds 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2568 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 18 sheets defined 19.1% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 38 through 53 Processing helix chain 'A' and resid 61 through 82 Proline residue: A 73 - end of helix Processing helix chain 'A' and resid 114 through 121 removed outlier: 4.111A pdb=" N TRP A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.679A pdb=" N HIS A 229 " --> pdb=" O PRO A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.633A pdb=" N ASN A 255 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 271 removed outlier: 3.695A pdb=" N LEU A 270 " --> pdb=" O PRO A 267 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 53 Processing helix chain 'a' and resid 61 through 82 Proline residue: a 73 - end of helix Processing helix chain 'a' and resid 114 through 121 removed outlier: 4.110A pdb=" N TRP a 118 " --> pdb=" O SER a 114 " (cutoff:3.500A) Processing helix chain 'a' and resid 226 through 230 removed outlier: 3.679A pdb=" N HIS a 229 " --> pdb=" O PRO a 226 " (cutoff:3.500A) Processing helix chain 'a' and resid 244 through 248 Processing helix chain 'a' and resid 252 through 256 removed outlier: 3.632A pdb=" N ASN a 255 " --> pdb=" O SER a 252 " (cutoff:3.500A) Processing helix chain 'a' and resid 267 through 271 removed outlier: 3.695A pdb=" N LEU a 270 " --> pdb=" O PRO a 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 53 Processing helix chain 'B' and resid 61 through 82 Proline residue: B 73 - end of helix Processing helix chain 'B' and resid 114 through 121 removed outlier: 4.110A pdb=" N TRP B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.679A pdb=" N HIS B 229 " --> pdb=" O PRO B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.633A pdb=" N ASN B 255 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 271 removed outlier: 3.695A pdb=" N LEU B 270 " --> pdb=" O PRO B 267 " (cutoff:3.500A) Processing helix chain 'b' and resid 38 through 53 Processing helix chain 'b' and resid 61 through 82 Proline residue: b 73 - end of helix Processing helix chain 'b' and resid 114 through 121 removed outlier: 4.112A pdb=" N TRP b 118 " --> pdb=" O SER b 114 " (cutoff:3.500A) Processing helix chain 'b' and resid 226 through 230 removed outlier: 3.679A pdb=" N HIS b 229 " --> pdb=" O PRO b 226 " (cutoff:3.500A) Processing helix chain 'b' and resid 244 through 248 Processing helix chain 'b' and resid 252 through 256 removed outlier: 3.633A pdb=" N ASN b 255 " --> pdb=" O SER b 252 " (cutoff:3.500A) Processing helix chain 'b' and resid 267 through 271 removed outlier: 3.694A pdb=" N LEU b 270 " --> pdb=" O PRO b 267 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6 removed outlier: 3.965A pdb=" N GLY A 3 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS A 14 " --> pdb=" O VAL A 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 35 removed outlier: 8.191A pdb=" N ASN A 166 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR A 158 " --> pdb=" O ASN A 166 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N TRP A 168 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 88 through 91 removed outlier: 6.424A pdb=" N ILE A 57 " --> pdb=" O ASP A 136 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLY A 56 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 330 removed outlier: 3.529A pdb=" N TRP A 330 " --> pdb=" O TYR A 323 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A 215 " --> pdb=" O MET A 275 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE A 277 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 9.740A pdb=" N GLU A 213 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ILE A 212 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ALA A 205 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA A 187 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA A 196 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER A 185 " --> pdb=" O ALA A 196 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER a 185 " --> pdb=" O ALA a 196 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA a 196 " --> pdb=" O SER a 185 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA a 187 " --> pdb=" O VAL a 194 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ALA a 205 " --> pdb=" O ILE a 212 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ILE a 212 " --> pdb=" O ALA a 205 " (cutoff:3.500A) removed outlier: 9.740A pdb=" N GLU a 213 " --> pdb=" O PHE a 277 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE a 277 " --> pdb=" O GLU a 213 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA a 215 " --> pdb=" O MET a 275 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP a 330 " --> pdb=" O TYR a 323 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 287 removed outlier: 5.897A pdb=" N THR A 284 " --> pdb=" O TRP A 311 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N CYS A 313 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL A 286 " --> pdb=" O CYS A 313 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS A 312 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG A 336 " --> pdb=" O CYS A 312 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'a' and resid 2 through 6 removed outlier: 3.966A pdb=" N GLY a 3 " --> pdb=" O GLY a 16 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS a 14 " --> pdb=" O VAL a 5 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 32 through 35 removed outlier: 8.191A pdb=" N ASN a 166 " --> pdb=" O TYR a 158 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR a 158 " --> pdb=" O ASN a 166 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N TRP a 168 " --> pdb=" O GLU a 156 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'a' and resid 88 through 91 removed outlier: 6.424A pdb=" N ILE a 57 " --> pdb=" O ASP a 136 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLY a 56 " --> pdb=" O ALA a 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'a' and resid 284 through 287 removed outlier: 5.898A pdb=" N THR a 284 " --> pdb=" O TRP a 311 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N CYS a 313 " --> pdb=" O THR a 284 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL a 286 " --> pdb=" O CYS a 313 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS a 312 " --> pdb=" O ARG a 336 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG a 336 " --> pdb=" O CYS a 312 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 2 through 6 removed outlier: 3.966A pdb=" N GLY B 3 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS B 14 " --> pdb=" O VAL B 5 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 32 through 35 removed outlier: 8.192A pdb=" N ASN B 166 " --> pdb=" O TYR B 158 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR B 158 " --> pdb=" O ASN B 166 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N TRP B 168 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 88 through 91 removed outlier: 6.423A pdb=" N ILE B 57 " --> pdb=" O ASP B 136 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLY B 56 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 329 through 330 removed outlier: 3.529A pdb=" N TRP B 330 " --> pdb=" O TYR B 323 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA B 215 " --> pdb=" O MET B 275 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE B 277 " --> pdb=" O GLU B 213 " (cutoff:3.500A) removed outlier: 9.740A pdb=" N GLU B 213 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ILE B 212 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ALA B 205 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA B 187 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA B 196 " --> pdb=" O SER B 185 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER B 185 " --> pdb=" O ALA B 196 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B 186 " --> pdb=" O ILE b 188 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER b 185 " --> pdb=" O ALA b 196 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA b 196 " --> pdb=" O SER b 185 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA b 187 " --> pdb=" O VAL b 194 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ALA b 205 " --> pdb=" O ILE b 212 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ILE b 212 " --> pdb=" O ALA b 205 " (cutoff:3.500A) removed outlier: 9.740A pdb=" N GLU b 213 " --> pdb=" O PHE b 277 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE b 277 " --> pdb=" O GLU b 213 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA b 215 " --> pdb=" O MET b 275 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TRP b 330 " --> pdb=" O TYR b 323 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 284 through 287 removed outlier: 5.898A pdb=" N THR B 284 " --> pdb=" O TRP B 311 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N CYS B 313 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL B 286 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS B 312 " --> pdb=" O ARG B 336 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG B 336 " --> pdb=" O CYS B 312 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'b' and resid 2 through 6 removed outlier: 3.966A pdb=" N GLY b 3 " --> pdb=" O GLY b 16 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS b 14 " --> pdb=" O VAL b 5 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'b' and resid 32 through 35 removed outlier: 8.192A pdb=" N ASN b 166 " --> pdb=" O TYR b 158 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR b 158 " --> pdb=" O ASN b 166 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N TRP b 168 " --> pdb=" O GLU b 156 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 88 through 91 removed outlier: 6.423A pdb=" N ILE b 57 " --> pdb=" O ASP b 136 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLY b 56 " --> pdb=" O ALA b 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 284 through 287 removed outlier: 5.897A pdb=" N THR b 284 " --> pdb=" O TRP b 311 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N CYS b 313 " --> pdb=" O THR b 284 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL b 286 " --> pdb=" O CYS b 313 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS b 312 " --> pdb=" O ARG b 336 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG b 336 " --> pdb=" O CYS b 312 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 271 hydrogen bonds defined for protein. 729 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: 1.52 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3592 1.35 - 1.47: 2750 1.47 - 1.59: 4890 1.59 - 1.71: 0 1.71 - 1.83: 120 Bond restraints: 11352 Sorted by residual: bond pdb=" CA GLU B 83 " pdb=" CB GLU B 83 " ideal model delta sigma weight residual 1.527 1.544 -0.017 1.70e-02 3.46e+03 1.02e+00 bond pdb=" CA GLU A 83 " pdb=" CB GLU A 83 " ideal model delta sigma weight residual 1.527 1.544 -0.017 1.70e-02 3.46e+03 9.53e-01 bond pdb=" CA GLU b 83 " pdb=" CB GLU b 83 " ideal model delta sigma weight residual 1.527 1.544 -0.017 1.70e-02 3.46e+03 9.50e-01 bond pdb=" CA GLU a 83 " pdb=" CB GLU a 83 " ideal model delta sigma weight residual 1.527 1.543 -0.016 1.70e-02 3.46e+03 8.65e-01 bond pdb=" CB LEU A 13 " pdb=" CG LEU A 13 " ideal model delta sigma weight residual 1.530 1.514 0.016 2.00e-02 2.50e+03 6.55e-01 ... (remaining 11347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 14940 1.56 - 3.13: 383 3.13 - 4.69: 37 4.69 - 6.26: 16 6.26 - 7.82: 8 Bond angle restraints: 15384 Sorted by residual: angle pdb=" N SER b 233 " pdb=" CA SER b 233 " pdb=" C SER b 233 " ideal model delta sigma weight residual 110.44 113.86 -3.42 1.20e+00 6.94e-01 8.12e+00 angle pdb=" N SER a 233 " pdb=" CA SER a 233 " pdb=" C SER a 233 " ideal model delta sigma weight residual 110.44 113.85 -3.41 1.20e+00 6.94e-01 8.06e+00 angle pdb=" N SER B 233 " pdb=" CA SER B 233 " pdb=" C SER B 233 " ideal model delta sigma weight residual 110.44 113.84 -3.40 1.20e+00 6.94e-01 8.01e+00 angle pdb=" N SER A 233 " pdb=" CA SER A 233 " pdb=" C SER A 233 " ideal model delta sigma weight residual 110.44 113.79 -3.35 1.20e+00 6.94e-01 7.78e+00 angle pdb=" CA LEU B 128 " pdb=" CB LEU B 128 " pdb=" CG LEU B 128 " ideal model delta sigma weight residual 116.30 124.12 -7.82 3.50e+00 8.16e-02 4.99e+00 ... (remaining 15379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 6253 17.87 - 35.75: 477 35.75 - 53.62: 65 53.62 - 71.50: 12 71.50 - 89.37: 18 Dihedral angle restraints: 6825 sinusoidal: 2845 harmonic: 3980 Sorted by residual: dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 312 " pdb=" CB CYS B 312 " ideal model delta sinusoidal sigma weight residual -86.00 -175.37 89.37 1 1.00e+01 1.00e-02 9.50e+01 dihedral pdb=" CB CYS b 291 " pdb=" SG CYS b 291 " pdb=" SG CYS b 312 " pdb=" CB CYS b 312 " ideal model delta sinusoidal sigma weight residual -86.00 -175.35 89.35 1 1.00e+01 1.00e-02 9.49e+01 dihedral pdb=" CB CYS a 291 " pdb=" SG CYS a 291 " pdb=" SG CYS a 312 " pdb=" CB CYS a 312 " ideal model delta sinusoidal sigma weight residual -86.00 -175.35 89.35 1 1.00e+01 1.00e-02 9.49e+01 ... (remaining 6822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1160 0.036 - 0.073: 326 0.073 - 0.109: 114 0.109 - 0.146: 40 0.146 - 0.182: 4 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CB ILE a 242 " pdb=" CA ILE a 242 " pdb=" CG1 ILE a 242 " pdb=" CG2 ILE a 242 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.31e-01 chirality pdb=" CB ILE B 242 " pdb=" CA ILE B 242 " pdb=" CG1 ILE B 242 " pdb=" CG2 ILE B 242 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.30e-01 chirality pdb=" CB ILE A 242 " pdb=" CA ILE A 242 " pdb=" CG1 ILE A 242 " pdb=" CG2 ILE A 242 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.19e-01 ... (remaining 1641 not shown) Planarity restraints: 1956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 68 " 0.014 2.00e-02 2.50e+03 1.51e-02 5.67e+00 pdb=" CG TRP A 68 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A 68 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 68 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 68 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 68 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 68 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 68 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 68 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 68 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP b 68 " -0.014 2.00e-02 2.50e+03 1.50e-02 5.65e+00 pdb=" CG TRP b 68 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP b 68 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP b 68 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP b 68 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP b 68 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP b 68 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP b 68 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP b 68 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP b 68 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 68 " -0.015 2.00e-02 2.50e+03 1.50e-02 5.62e+00 pdb=" CG TRP B 68 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP B 68 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP B 68 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 68 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 68 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 68 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 68 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 68 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 68 " -0.000 2.00e-02 2.50e+03 ... (remaining 1953 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 959 2.74 - 3.28: 11170 3.28 - 3.82: 18502 3.82 - 4.36: 21528 4.36 - 4.90: 36499 Nonbonded interactions: 88658 Sorted by model distance: nonbonded pdb=" NZ LYS B 170 " pdb=" O LEU B 171 " model vdw 2.206 3.120 nonbonded pdb=" NZ LYS A 170 " pdb=" O LEU A 171 " model vdw 2.206 3.120 nonbonded pdb=" NZ LYS a 170 " pdb=" O LEU a 171 " model vdw 2.207 3.120 nonbonded pdb=" NZ LYS b 170 " pdb=" O LEU b 171 " model vdw 2.207 3.120 nonbonded pdb=" O ILE b 212 " pdb=" NH1 ARG b 257 " model vdw 2.273 3.120 ... (remaining 88653 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' selection = chain 'B' selection = chain 'b' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'a' selection = chain 'B' selection = chain 'b' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.170 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4285 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 : 0.010 0.590 11379 Z= 0.476 Angle : 0.714 23.926 15438 Z= 0.363 Chirality : 0.042 0.182 1644 Planarity : 0.003 0.017 1956 Dihedral : 12.435 83.112 4176 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.59 (0.21), residues: 1376 helix: 1.54 (0.47), residues: 156 sheet: 0.35 (0.31), residues: 280 loop : -1.01 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 272 TYR 0.008 0.001 TYR B 158 PHE 0.004 0.001 PHE A 133 TRP 0.041 0.002 TRP A 68 HIS 0.003 0.001 HIS a 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.11 (11352) covalent geometry : angle 0.59474 / 0.31 (15384) SS BOND : bond 0.19036 / 9.41 ( 27) SS BOND : angle 6.70093 / 4.17 ( 54) hydrogen bonds : bond 0.20452 / 13.52 ( 271) hydrogen bonds : angle 9.52350 / 6.55 ( 729) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.070 Fit side-chains REVERT: A 46 ILE cc_start: 0.8343 (pt) cc_final: 0.7945 (pt) REVERT: A 48 LYS cc_start: 0.9012 (pttm) cc_final: 0.8576 (pptt) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0800 time to fit residues: 4.0008 Evaluate side-chains 28 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.0470 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 HIS A 107 GLN A 131 HIS A 175 GLN A 195 HIS A 224 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.108114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.085244 restraints weight = 13594.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.087897 restraints weight = 10004.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.089998 restraints weight = 7885.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.091352 restraints weight = 6527.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.092616 restraints weight = 5677.417| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5810 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.598 11379 Z= 0.477 Angle : 0.664 24.355 15438 Z= 0.332 Chirality : 0.041 0.170 1644 Planarity : 0.004 0.055 1956 Dihedral : 4.167 23.705 1472 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.58 (0.21), residues: 1376 helix: 1.99 (0.47), residues: 156 sheet: -0.22 (0.29), residues: 288 loop : -0.89 (0.18), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG a 105 TYR 0.007 0.001 TYR B 323 PHE 0.010 0.001 PHE b 217 TRP 0.019 0.002 TRP a 8 HIS 0.003 0.001 HIS A 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (11352) covalent geometry : angle 0.53559 / 0.27 (15384) SS BOND : bond 0.19033 / 9.41 ( 27) SS BOND : angle 6.66746 / 4.13 ( 54) hydrogen bonds : bond 0.05363 / 3.24 ( 271) hydrogen bonds : angle 7.31910 / 4.99 ( 729) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 124 LEU cc_start: 0.6546 (mt) cc_final: 0.5827 (pp) REVERT: a 184 MET cc_start: 0.7253 (tpt) cc_final: 0.6654 (tpp) REVERT: a 323 TYR cc_start: 0.8480 (m-10) cc_final: 0.8073 (m-10) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0678 time to fit residues: 3.9611 Evaluate side-chains 32 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 134 optimal weight: 3.9990 chunk 105 optimal weight: 0.0870 chunk 31 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 131 HIS a 175 GLN a 224 HIS ** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.096308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.067230 restraints weight = 16966.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.069492 restraints weight = 13239.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.071216 restraints weight = 11020.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.072533 restraints weight = 9601.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.073551 restraints weight = 8610.736| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6039 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.602 11379 Z= 0.475 Angle : 0.685 23.842 15438 Z= 0.347 Chirality : 0.042 0.152 1644 Planarity : 0.004 0.044 1956 Dihedral : 4.016 20.499 1472 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.63 (0.21), residues: 1376 helix: 1.52 (0.46), residues: 156 sheet: -0.39 (0.29), residues: 292 loop : -0.78 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 257 TYR 0.008 0.001 TYR A 260 PHE 0.022 0.002 PHE a 20 TRP 0.035 0.002 TRP A 68 HIS 0.005 0.001 HIS a 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (11352) covalent geometry : angle 0.56176 / 0.29 (15384) SS BOND : bond 0.19018 / 9.41 ( 27) SS BOND : angle 6.64080 / 4.15 ( 54) hydrogen bonds : bond 0.05407 / 3.25 ( 271) hydrogen bonds : angle 6.94982 / 4.76 ( 729) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 PHE cc_start: 0.8856 (m-10) cc_final: 0.8614 (m-10) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0666 time to fit residues: 3.2487 Evaluate side-chains 24 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 95 optimal weight: 0.0070 chunk 80 optimal weight: 0.6980 chunk 127 optimal weight: 0.0470 chunk 129 optimal weight: 0.2980 chunk 12 optimal weight: 10.0000 chunk 62 optimal weight: 0.0040 chunk 33 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 25 optimal weight: 0.0980 chunk 35 optimal weight: 2.9990 overall best weight: 0.0908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN B 131 HIS B 175 GLN B 253 GLN ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.110239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.092847 restraints weight = 23139.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.094641 restraints weight = 17373.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.096161 restraints weight = 14026.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.097125 restraints weight = 11833.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.097755 restraints weight = 10371.418| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5830 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.601 11379 Z= 0.476 Angle : 0.739 23.513 15438 Z= 0.368 Chirality : 0.043 0.211 1644 Planarity : 0.004 0.031 1956 Dihedral : 4.107 24.056 1472 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.75 (0.21), residues: 1376 helix: 1.31 (0.45), residues: 156 sheet: -0.49 (0.29), residues: 300 loop : -0.83 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG a 294 TYR 0.031 0.002 TYR A 256 PHE 0.008 0.001 PHE B 133 TRP 0.015 0.001 TRP B 68 HIS 0.002 0.001 HIS a 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (11352) covalent geometry : angle 0.61525 / 0.31 (15384) SS BOND : bond 0.19016 / 9.41 ( 27) SS BOND : angle 6.94306 / 4.34 ( 54) hydrogen bonds : bond 0.05191 / 3.12 ( 271) hydrogen bonds : angle 6.61281 / 4.57 ( 729) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 97 MET cc_start: 0.5955 (tmm) cc_final: 0.5710 (tmm) REVERT: B 123 MET cc_start: 0.1318 (mmp) cc_final: 0.0351 (mmt) REVERT: B 217 PHE cc_start: 0.8776 (m-10) cc_final: 0.8471 (m-80) REVERT: B 323 TYR cc_start: 0.8353 (m-80) cc_final: 0.7486 (m-80) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0537 time to fit residues: 2.1539 Evaluate side-chains 21 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 131 optimal weight: 0.0970 chunk 49 optimal weight: 0.0020 chunk 125 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 44 optimal weight: 0.0980 chunk 101 optimal weight: 0.0020 chunk 120 optimal weight: 6.9990 chunk 126 optimal weight: 0.0670 chunk 52 optimal weight: 4.9990 overall best weight: 0.0532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN B 151 ASN B 224 HIS B 253 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.110878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.093296 restraints weight = 22637.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.095147 restraints weight = 17140.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.096524 restraints weight = 13879.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.097315 restraints weight = 11758.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.098119 restraints weight = 10442.316| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5797 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.602 11379 Z= 0.474 Angle : 0.683 23.393 15438 Z= 0.348 Chirality : 0.043 0.182 1644 Planarity : 0.003 0.027 1956 Dihedral : 3.902 19.016 1472 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.76 (0.21), residues: 1376 helix: 1.03 (0.44), residues: 156 sheet: -0.49 (0.30), residues: 300 loop : -0.78 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG a 294 TYR 0.031 0.002 TYR b 256 PHE 0.006 0.001 PHE B 133 TRP 0.047 0.002 TRP B 68 HIS 0.003 0.001 HIS a 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (11352) covalent geometry : angle 0.56528 / 0.30 (15384) SS BOND : bond 0.19015 / 9.41 ( 27) SS BOND : angle 6.51644 / 4.07 ( 54) hydrogen bonds : bond 0.05093 / 3.06 ( 271) hydrogen bonds : angle 6.53634 / 4.51 ( 729) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 97 MET cc_start: 0.6044 (tmm) cc_final: 0.5725 (tmm) REVERT: B 123 MET cc_start: 0.1189 (mmp) cc_final: 0.0193 (mmt) REVERT: B 217 PHE cc_start: 0.8788 (m-10) cc_final: 0.8456 (m-80) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0558 time to fit residues: 2.0995 Evaluate side-chains 23 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 25 optimal weight: 0.5980 chunk 30 optimal weight: 0.0470 chunk 103 optimal weight: 0.0770 chunk 53 optimal weight: 2.9990 chunk 79 optimal weight: 0.0170 chunk 3 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.2474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.110768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.093765 restraints weight = 22927.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.095533 restraints weight = 17071.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.096963 restraints weight = 13647.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.097945 restraints weight = 11432.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.098569 restraints weight = 9963.922| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5802 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.601 11379 Z= 0.473 Angle : 0.674 23.282 15438 Z= 0.340 Chirality : 0.042 0.137 1644 Planarity : 0.003 0.026 1956 Dihedral : 3.826 18.347 1472 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.33 % Allowed : 1.64 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.70 (0.21), residues: 1376 helix: 1.03 (0.44), residues: 156 sheet: 0.02 (0.32), residues: 260 loop : -0.90 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG a 294 TYR 0.020 0.001 TYR A 256 PHE 0.007 0.001 PHE a 178 TRP 0.027 0.001 TRP A 68 HIS 0.004 0.001 HIS B 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (11352) covalent geometry : angle 0.55056 / 0.28 (15384) SS BOND : bond 0.19010 / 9.40 ( 27) SS BOND : angle 6.60187 / 4.13 ( 54) hydrogen bonds : bond 0.04859 / 2.92 ( 271) hydrogen bonds : angle 6.29646 / 4.36 ( 729) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 MET cc_start: 0.5935 (tmm) cc_final: 0.5663 (tmm) REVERT: B 123 MET cc_start: 0.1236 (mmp) cc_final: 0.0279 (mmt) REVERT: B 217 PHE cc_start: 0.8835 (m-10) cc_final: 0.8546 (m-80) outliers start: 1 outliers final: 0 residues processed: 33 average time/residue: 0.0841 time to fit residues: 3.3442 Evaluate side-chains 23 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 40 optimal weight: 0.9980 chunk 75 optimal weight: 0.2980 chunk 11 optimal weight: 0.0570 chunk 83 optimal weight: 0.0040 chunk 100 optimal weight: 0.2980 chunk 108 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 110 optimal weight: 0.6980 chunk 17 optimal weight: 0.0070 chunk 84 optimal weight: 0.6980 overall best weight: 0.1328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.110582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.093450 restraints weight = 22881.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.095409 restraints weight = 17161.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.096749 restraints weight = 13763.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.097686 restraints weight = 11632.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.098446 restraints weight = 10166.584| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5777 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.601 11379 Z= 0.472 Angle : 0.666 23.170 15438 Z= 0.330 Chirality : 0.042 0.155 1644 Planarity : 0.003 0.025 1956 Dihedral : 3.694 17.648 1472 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 (0.21), residues: 1376 helix: 1.27 (0.46), residues: 156 sheet: 0.00 (0.31), residues: 260 loop : -0.84 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG a 294 TYR 0.015 0.001 TYR a 256 PHE 0.004 0.001 PHE a 133 TRP 0.023 0.001 TRP A 68 HIS 0.003 0.001 HIS a 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.09 (11352) covalent geometry : angle 0.54315 / 0.27 (15384) SS BOND : bond 0.19008 / 9.40 ( 27) SS BOND : angle 6.54457 / 4.09 ( 54) hydrogen bonds : bond 0.04819 / 2.88 ( 271) hydrogen bonds : angle 5.92497 / 4.11 ( 729) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 MET cc_start: 0.6016 (tmm) cc_final: 0.5698 (tmm) REVERT: B 123 MET cc_start: 0.1141 (mmp) cc_final: 0.0162 (mmt) REVERT: B 217 PHE cc_start: 0.8824 (m-10) cc_final: 0.8569 (m-80) REVERT: B 323 TYR cc_start: 0.8042 (m-80) cc_final: 0.7434 (m-80) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0815 time to fit residues: 2.9540 Evaluate side-chains 24 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 51 optimal weight: 0.0670 chunk 18 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 56 optimal weight: 0.0870 chunk 76 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 overall best weight: 2.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.103371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.086662 restraints weight = 23667.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.088372 restraints weight = 17793.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.089696 restraints weight = 14320.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.090641 restraints weight = 12062.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.091359 restraints weight = 10588.338| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5958 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.605 11379 Z= 0.484 Angle : 0.700 23.096 15438 Z= 0.362 Chirality : 0.042 0.155 1644 Planarity : 0.004 0.030 1956 Dihedral : 4.116 18.082 1472 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -1.06 (0.21), residues: 1376 helix: 0.61 (0.44), residues: 156 sheet: -0.97 (0.35), residues: 176 loop : -0.91 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG a 324 TYR 0.006 0.001 TYR b 200 PHE 0.013 0.002 PHE B 178 TRP 0.060 0.002 TRP a 68 HIS 0.008 0.002 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (11352) covalent geometry : angle 0.58664 / 0.31 (15384) SS BOND : bond 0.19010 / 9.41 ( 27) SS BOND : angle 6.49165 / 4.05 ( 54) hydrogen bonds : bond 0.05126 / 3.09 ( 271) hydrogen bonds : angle 6.83426 / 4.71 ( 729) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 MET cc_start: 0.6416 (tmm) cc_final: 0.6117 (tmm) REVERT: B 123 MET cc_start: 0.1040 (mmp) cc_final: -0.0115 (mmt) REVERT: B 217 PHE cc_start: 0.8877 (m-10) cc_final: 0.8515 (m-10) REVERT: B 323 TYR cc_start: 0.8310 (m-80) cc_final: 0.7741 (m-80) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0736 time to fit residues: 2.5763 Evaluate side-chains 22 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 107 optimal weight: 0.0030 chunk 79 optimal weight: 0.6980 chunk 11 optimal weight: 0.0470 chunk 23 optimal weight: 0.2980 chunk 134 optimal weight: 0.0970 chunk 4 optimal weight: 6.9990 chunk 56 optimal weight: 0.0000 chunk 92 optimal weight: 0.6980 chunk 50 optimal weight: 0.3980 chunk 18 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 overall best weight: 0.0890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.092413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.069628 restraints weight = 19341.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.071643 restraints weight = 15030.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.073156 restraints weight = 12436.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.074318 restraints weight = 10751.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.075144 restraints weight = 9585.922| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5974 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.601 11379 Z= 0.473 Angle : 0.684 23.112 15438 Z= 0.345 Chirality : 0.043 0.142 1644 Planarity : 0.003 0.023 1956 Dihedral : 3.711 17.493 1472 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.77 (0.21), residues: 1376 helix: 0.85 (0.44), residues: 156 sheet: -0.33 (0.31), residues: 272 loop : -0.81 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG b 257 TYR 0.011 0.001 TYR a 256 PHE 0.005 0.001 PHE A 20 TRP 0.046 0.002 TRP a 68 HIS 0.004 0.001 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (11352) covalent geometry : angle 0.56680 / 0.29 (15384) SS BOND : bond 0.19007 / 9.40 ( 27) SS BOND : angle 6.50540 / 4.05 ( 54) hydrogen bonds : bond 0.04865 / 2.95 ( 271) hydrogen bonds : angle 6.26645 / 4.35 ( 729) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 97 MET cc_start: 0.6645 (tmm) cc_final: 0.6233 (tmm) REVERT: B 123 MET cc_start: 0.1413 (mmp) cc_final: 0.0342 (mmt) REVERT: B 217 PHE cc_start: 0.8915 (m-10) cc_final: 0.8510 (m-80) REVERT: B 275 MET cc_start: 0.8928 (mmm) cc_final: 0.8433 (mmp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0727 time to fit residues: 2.6060 Evaluate side-chains 22 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 1 optimal weight: 4.9990 chunk 89 optimal weight: 0.0370 chunk 5 optimal weight: 8.9990 chunk 24 optimal weight: 0.4980 chunk 115 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 chunk 111 optimal weight: 7.9990 chunk 128 optimal weight: 0.9980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.090436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.064927 restraints weight = 17024.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.066877 restraints weight = 13440.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.068357 restraints weight = 11283.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.069527 restraints weight = 9832.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.070418 restraints weight = 8821.592| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6017 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.601 11379 Z= 0.472 Angle : 0.674 22.991 15438 Z= 0.340 Chirality : 0.042 0.142 1644 Planarity : 0.003 0.022 1956 Dihedral : 3.705 17.120 1472 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.90 (0.21), residues: 1376 helix: 0.77 (0.44), residues: 156 sheet: -0.36 (0.38), residues: 172 loop : -0.91 (0.17), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 294 TYR 0.012 0.001 TYR b 256 PHE 0.005 0.001 PHE B 20 TRP 0.043 0.002 TRP a 68 HIS 0.004 0.001 HIS a 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.09 (11352) covalent geometry : angle 0.55496 / 0.29 (15384) SS BOND : bond 0.19006 / 9.40 ( 27) SS BOND : angle 6.49405 / 4.05 ( 54) hydrogen bonds : bond 0.04908 / 2.98 ( 271) hydrogen bonds : angle 6.33837 / 4.43 ( 729) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 97 MET cc_start: 0.6585 (tmm) cc_final: 0.6188 (tmm) REVERT: B 123 MET cc_start: 0.1880 (mmp) cc_final: 0.0827 (mmt) REVERT: B 178 PHE cc_start: 0.9197 (m-80) cc_final: 0.8973 (m-10) REVERT: B 217 PHE cc_start: 0.9150 (m-10) cc_final: 0.8613 (m-80) REVERT: B 275 MET cc_start: 0.9073 (mmm) cc_final: 0.7687 (mmp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0575 time to fit residues: 2.0810 Evaluate side-chains 23 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 4.9990 chunk 71 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 27 optimal weight: 0.0020 chunk 76 optimal weight: 6.9990 chunk 15 optimal weight: 0.0870 chunk 23 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 25 optimal weight: 0.0770 overall best weight: 0.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 253 GLN ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.091991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.066651 restraints weight = 16446.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.068357 restraints weight = 13347.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.069697 restraints weight = 11384.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.070736 restraints weight = 10054.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.071244 restraints weight = 9123.018| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6009 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.601 11379 Z= 0.471 Angle : 0.662 22.947 15438 Z= 0.334 Chirality : 0.042 0.144 1644 Planarity : 0.003 0.022 1956 Dihedral : 3.551 16.217 1472 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.82 (0.21), residues: 1376 helix: 0.76 (0.44), residues: 156 sheet: -0.14 (0.32), residues: 252 loop : -0.92 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG b 294 TYR 0.026 0.002 TYR a 323 PHE 0.005 0.001 PHE B 20 TRP 0.042 0.002 TRP A 68 HIS 0.003 0.001 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 (11352) covalent geometry : angle 0.54045 / 0.28 (15384) SS BOND : bond 0.19003 / 9.40 ( 27) SS BOND : angle 6.50027 / 4.05 ( 54) hydrogen bonds : bond 0.04836 / 2.93 ( 271) hydrogen bonds : angle 6.04834 / 4.22 ( 729) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1270.64 seconds wall clock time: 22 minutes 56.10 seconds (1376.10 seconds total)