Starting phenix.real_space_refine on Thu Jun 4 07:05:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w1x_65558/06_2026/9w1x_65558.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w1x_65558/06_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 { model { file = "/net/cci-nas-00/data/ceres_data/9w1x_65558/06_2026/9w1x_65558.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w1x_65558/06_2026/9w1x_65558.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w1x_65558/06_2026/9w1x_65558.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w1x_65558/06_2026/9w1x_65558.map" } 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-6079/lib/python3.9/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: 2.66, per 1000 atoms: 0.24 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 536.1 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: 0.42 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: 1.66 Time building geometry restraints manager: 1.15 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: 0.03 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: 6.390 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.340 Find NCS groups from input model: 0.090 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4533 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 : 0.108 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: 0.0936 time to fit residues: 4.6513 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 : 0.107 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4324 r_free = 0.4324 target = 0.109787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.089480 restraints weight = 15437.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.091946 restraints weight = 11642.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.093649 restraints weight = 9317.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.094991 restraints weight = 7838.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.095960 restraints weight = 6829.049| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5911 moved from start: 0.2355 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 : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.33 % Allowed : 3.95 % Favored : 95.72 % 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) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 124 LEU cc_start: 0.6519 (mt) cc_final: 0.5797 (pp) REVERT: a 184 MET cc_start: 0.7268 (tpt) cc_final: 0.6619 (tpp) REVERT: a 323 TYR cc_start: 0.8535 (m-10) cc_final: 0.8093 (m-10) outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.1003 time to fit residues: 5.8414 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 : 0.118 ------------------------------------------------------------------------------- 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: 0.3980 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: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** 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 = 0.4321 r_free = 0.4321 target = 0.110820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.093583 restraints weight = 23376.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.095370 restraints weight = 17549.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.096738 restraints weight = 14129.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.097680 restraints weight = 11898.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.098141 restraints weight = 10414.007| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5932 moved from start: 0.2940 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 23.907 15438 Z= 0.345 Chirality : 0.042 0.137 1644 Planarity : 0.003 0.043 1956 Dihedral : 3.941 20.343 1472 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.33 % Allowed : 4.28 % Favored : 95.39 % 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: -0.78 (0.21), residues: 1376 helix: 1.48 (0.46), residues: 156 sheet: -0.46 (0.29), residues: 292 loop : -0.92 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 257 TYR 0.007 0.001 TYR A 260 PHE 0.021 0.001 PHE b 20 TRP 0.036 0.001 TRP A 68 HIS 0.003 0.001 HIS a 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (11352) covalent geometry : angle 0.55953 / 0.29 (15384) SS BOND : bond 0.19019 / 9.41 ( 27) SS BOND : angle 6.63289 / 4.15 ( 54) hydrogen bonds : bond 0.05441 / 3.28 ( 271) hydrogen bonds : angle 6.77985 / 4.65 ( 729) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 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: 1 poor density : 42 time to evaluate : 0.109 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 0.0845 time to fit residues: 4.3229 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 : 0.116 ------------------------------------------------------------------------------- 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: 0.0000 chunk 80 optimal weight: 9.9990 chunk 127 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 62 optimal weight: 0.0050 chunk 33 optimal weight: 0.0000 chunk 54 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 overall best weight: 0.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN B 82 ASN ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.110754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.093360 restraints weight = 22747.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.095318 restraints weight = 17242.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.096751 restraints weight = 13864.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.097800 restraints weight = 11631.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.098568 restraints weight = 10120.066| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5880 moved from start: 0.3170 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 : 0.710 23.408 15438 Z= 0.351 Chirality : 0.043 0.189 1644 Planarity : 0.004 0.030 1956 Dihedral : 4.072 23.497 1472 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % 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: -1.25 (0.21), residues: 1376 helix: 0.79 (0.43), residues: 156 sheet: -0.86 (0.29), residues: 304 loop : -1.14 (0.18), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 174 TYR 0.031 0.002 TYR a 256 PHE 0.008 0.001 PHE B 133 TRP 0.014 0.001 TRP B 68 HIS 0.005 0.001 HIS B 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (11352) covalent geometry : angle 0.58748 / 0.30 (15384) SS BOND : bond 0.19015 / 9.41 ( 27) SS BOND : angle 6.77295 / 4.24 ( 54) hydrogen bonds : bond 0.05071 / 3.04 ( 271) hydrogen bonds : angle 6.39918 / 4.43 ( 729) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 MET cc_start: 0.5962 (tmm) cc_final: 0.5705 (tmm) REVERT: B 123 MET cc_start: 0.1128 (mmp) cc_final: 0.0115 (mmt) REVERT: B 323 TYR cc_start: 0.8313 (m-80) cc_final: 0.7576 (m-80) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0648 time to fit residues: 2.5920 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 0.0030 chunk 131 optimal weight: 0.7980 chunk 49 optimal weight: 0.0770 chunk 125 optimal weight: 2.9990 chunk 95 optimal weight: 0.3980 chunk 44 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 chunk 126 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 overall best weight: 0.3948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN B 253 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.110509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.093259 restraints weight = 22363.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.095049 restraints weight = 16876.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.096486 restraints weight = 13675.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.097456 restraints weight = 11527.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.098260 restraints weight = 10079.037| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5835 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.603 11379 Z= 0.472 Angle : 0.655 23.367 15438 Z= 0.328 Chirality : 0.042 0.185 1644 Planarity : 0.003 0.025 1956 Dihedral : 3.838 19.021 1472 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % 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: -1.29 (0.21), residues: 1376 helix: 0.51 (0.42), residues: 156 sheet: -0.79 (0.30), residues: 300 loop : -1.15 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG a 294 TYR 0.026 0.001 TYR A 256 PHE 0.005 0.001 PHE B 133 TRP 0.048 0.002 TRP B 68 HIS 0.003 0.001 HIS B 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.09 (11352) covalent geometry : angle 0.53199 / 0.27 (15384) SS BOND : bond 0.19016 / 9.41 ( 27) SS BOND : angle 6.49287 / 4.05 ( 54) hydrogen bonds : bond 0.04949 / 2.95 ( 271) hydrogen bonds : angle 6.22999 / 4.32 ( 729) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 97 MET cc_start: 0.5411 (tmm) cc_final: 0.5048 (tmm) REVERT: B 123 MET cc_start: 0.2113 (mmp) cc_final: 0.1160 (mmt) REVERT: B 217 PHE cc_start: 0.9034 (m-80) cc_final: 0.8834 (m-80) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0716 time to fit residues: 2.9878 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 : 0.122 ------------------------------------------------------------------------------- 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: 5.9990 chunk 30 optimal weight: 0.0980 chunk 103 optimal weight: 0.2980 chunk 53 optimal weight: 0.2980 chunk 79 optimal weight: 0.0570 chunk 3 optimal weight: 0.0040 chunk 29 optimal weight: 4.9990 chunk 92 optimal weight: 0.0970 chunk 135 optimal weight: 0.7980 chunk 56 optimal weight: 0.0870 chunk 7 optimal weight: 0.0060 overall best weight: 0.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 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 = 0.4318 r_free = 0.4318 target = 0.110629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.093448 restraints weight = 22668.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.095451 restraints weight = 16897.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.096903 restraints weight = 13440.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.097797 restraints weight = 11233.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.098652 restraints weight = 9833.366| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5879 moved from start: 0.3595 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 : 0.649 23.239 15438 Z= 0.321 Chirality : 0.041 0.137 1644 Planarity : 0.003 0.024 1956 Dihedral : 3.734 18.256 1472 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % 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: -1.47 (0.21), residues: 1376 helix: 0.34 (0.43), residues: 156 sheet: -0.91 (0.29), residues: 316 loop : -1.28 (0.18), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG a 294 TYR 0.022 0.001 TYR a 256 PHE 0.004 0.001 PHE B 133 TRP 0.029 0.001 TRP A 68 HIS 0.003 0.001 HIS b 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.09 (11352) covalent geometry : angle 0.52023 / 0.26 (15384) SS BOND : bond 0.19009 / 9.40 ( 27) SS BOND : angle 6.56870 / 4.11 ( 54) hydrogen bonds : bond 0.04814 / 2.90 ( 271) hydrogen bonds : angle 5.94339 / 4.13 ( 729) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 MET cc_start: 0.6136 (tmm) cc_final: 0.5848 (tmm) REVERT: B 123 MET cc_start: 0.1137 (mmp) cc_final: 0.0127 (mmt) REVERT: B 217 PHE cc_start: 0.8811 (m-80) cc_final: 0.8538 (m-80) outliers start: 1 outliers final: 0 residues processed: 32 average time/residue: 0.0630 time to fit residues: 2.5525 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 : 0.130 ------------------------------------------------------------------------------- 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: 0.7980 chunk 75 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 83 optimal weight: 0.1980 chunk 100 optimal weight: 0.0010 chunk 108 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 HIS B 253 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.109607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.092462 restraints weight = 22965.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.094454 restraints weight = 16898.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.096021 restraints weight = 13394.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.096910 restraints weight = 11112.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.097789 restraints weight = 9719.053| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5914 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.602 11379 Z= 0.471 Angle : 0.641 23.029 15438 Z= 0.313 Chirality : 0.041 0.129 1644 Planarity : 0.003 0.022 1956 Dihedral : 3.727 17.688 1472 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % 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: -1.41 (0.21), residues: 1376 helix: 0.53 (0.43), residues: 156 sheet: -0.60 (0.31), residues: 272 loop : -1.37 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG b 294 TYR 0.016 0.001 TYR a 256 PHE 0.007 0.001 PHE a 178 TRP 0.024 0.001 TRP A 68 HIS 0.003 0.001 HIS B 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.08 (11352) covalent geometry : angle 0.51333 / 0.25 (15384) SS BOND : bond 0.19010 / 9.40 ( 27) SS BOND : angle 6.52454 / 4.08 ( 54) hydrogen bonds : bond 0.04695 / 2.82 ( 271) hydrogen bonds : angle 5.62914 / 3.92 ( 729) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 MET cc_start: 0.5975 (tmm) cc_final: 0.5619 (tmm) REVERT: B 123 MET cc_start: 0.1375 (mmp) cc_final: 0.0398 (mmt) REVERT: B 217 PHE cc_start: 0.9041 (m-80) cc_final: 0.8764 (m-80) REVERT: B 323 TYR cc_start: 0.8538 (m-80) cc_final: 0.7551 (m-80) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0919 time to fit residues: 3.4855 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 : 0.115 ------------------------------------------------------------------------------- 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: 0.7980 chunk 18 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 71 optimal weight: 0.0970 chunk 56 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 overall best weight: 1.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.106994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.089674 restraints weight = 23414.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.091602 restraints weight = 17286.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.093081 restraints weight = 13727.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.094068 restraints weight = 11474.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.094648 restraints weight = 10006.994| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5984 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.604 11379 Z= 0.473 Angle : 0.644 22.969 15438 Z= 0.320 Chirality : 0.040 0.130 1644 Planarity : 0.003 0.023 1956 Dihedral : 3.740 17.417 1472 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % 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: -1.49 (0.20), residues: 1376 helix: 0.24 (0.43), residues: 156 sheet: -0.76 (0.42), residues: 144 loop : -1.31 (0.17), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG a 294 TYR 0.013 0.001 TYR A 256 PHE 0.006 0.001 PHE b 34 TRP 0.062 0.002 TRP a 68 HIS 0.004 0.001 HIS b 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (11352) covalent geometry : angle 0.51829 / 0.26 (15384) SS BOND : bond 0.19005 / 9.40 ( 27) SS BOND : angle 6.48190 / 4.05 ( 54) hydrogen bonds : bond 0.04731 / 2.84 ( 271) hydrogen bonds : angle 5.91730 / 4.13 ( 729) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 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 : 0.127 Fit side-chains revert: symmetry clash REVERT: B 97 MET cc_start: 0.6010 (tmm) cc_final: 0.5625 (tmm) REVERT: B 123 MET cc_start: 0.1721 (mmp) cc_final: 0.0724 (mmt) REVERT: B 178 PHE cc_start: 0.9172 (m-80) cc_final: 0.8944 (m-10) REVERT: B 217 PHE cc_start: 0.9090 (m-80) cc_final: 0.8826 (m-80) REVERT: B 245 LYS cc_start: 0.9367 (tmtt) cc_final: 0.9038 (mmtt) REVERT: B 323 TYR cc_start: 0.8684 (m-80) cc_final: 0.7777 (m-80) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0805 time to fit residues: 3.0083 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 : 0.109 ------------------------------------------------------------------------------- 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: 0.0670 chunk 79 optimal weight: 0.0970 chunk 11 optimal weight: 0.0970 chunk 23 optimal weight: 0.0770 chunk 134 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 0.0070 chunk 92 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 18 optimal weight: 8.9990 chunk 97 optimal weight: 0.0870 overall best weight: 0.0670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** 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 = 0.4148 r_free = 0.4148 target = 0.092434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.066484 restraints weight = 16976.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.068555 restraints weight = 13210.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.070118 restraints weight = 10964.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.071254 restraints weight = 9521.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.072172 restraints weight = 8551.388| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6063 moved from start: 0.4051 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 : 0.646 22.983 15438 Z= 0.319 Chirality : 0.041 0.136 1644 Planarity : 0.004 0.047 1956 Dihedral : 3.659 16.478 1472 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % 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: -1.71 (0.20), residues: 1376 helix: 0.32 (0.43), residues: 156 sheet: -1.34 (0.38), residues: 156 loop : -1.43 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG b 294 TYR 0.023 0.001 TYR B 256 PHE 0.005 0.001 PHE A 277 TRP 0.050 0.002 TRP a 68 HIS 0.003 0.001 HIS a 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.09 (11352) covalent geometry : angle 0.52162 / 0.26 (15384) SS BOND : bond 0.19004 / 9.40 ( 27) SS BOND : angle 6.47416 / 4.04 ( 54) hydrogen bonds : bond 0.04724 / 2.86 ( 271) hydrogen bonds : angle 5.69015 / 3.98 ( 729) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 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: symmetry clash REVERT: B 97 MET cc_start: 0.6373 (tmm) cc_final: 0.5994 (tmm) REVERT: B 123 MET cc_start: 0.1778 (mmp) cc_final: 0.0757 (mmt) REVERT: B 217 PHE cc_start: 0.9183 (m-80) cc_final: 0.8905 (m-80) REVERT: B 323 TYR cc_start: 0.8399 (m-80) cc_final: 0.7479 (m-80) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0641 time to fit residues: 2.3154 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 : 0.105 ------------------------------------------------------------------------------- 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: 3.9990 chunk 89 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 111 optimal weight: 0.0030 chunk 128 optimal weight: 0.9980 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** 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 = 0.4132 r_free = 0.4132 target = 0.091594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.066538 restraints weight = 17499.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.068474 restraints weight = 13786.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.069815 restraints weight = 11504.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.070972 restraints weight = 10055.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.071902 restraints weight = 9040.705| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6094 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.602 11379 Z= 0.470 Angle : 0.621 22.758 15438 Z= 0.308 Chirality : 0.040 0.126 1644 Planarity : 0.003 0.040 1956 Dihedral : 3.516 16.287 1472 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: -1.70 (0.20), residues: 1376 helix: 0.29 (0.43), residues: 156 sheet: -0.90 (0.46), residues: 124 loop : -1.50 (0.16), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG b 294 TYR 0.011 0.001 TYR A 256 PHE 0.005 0.001 PHE b 34 TRP 0.049 0.002 TRP A 68 HIS 0.002 0.001 HIS b 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.08 (11352) covalent geometry : angle 0.49198 / 0.25 (15384) SS BOND : bond 0.19002 / 9.40 ( 27) SS BOND : angle 6.43630 / 4.01 ( 54) hydrogen bonds : bond 0.04646 / 2.81 ( 271) hydrogen bonds : angle 5.68451 / 3.98 ( 729) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 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 : 0.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 MET cc_start: 0.6355 (tmm) cc_final: 0.5934 (tmm) REVERT: B 123 MET cc_start: 0.1900 (mmp) cc_final: 0.0859 (mmt) REVERT: B 178 PHE cc_start: 0.9173 (m-80) cc_final: 0.8970 (m-10) REVERT: B 217 PHE cc_start: 0.9209 (m-80) cc_final: 0.8829 (m-80) REVERT: B 323 TYR cc_start: 0.8555 (m-80) cc_final: 0.7869 (m-80) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0563 time to fit residues: 2.0818 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.9990 chunk 71 optimal weight: 0.0270 chunk 38 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 15 optimal weight: 0.0050 chunk 23 optimal weight: 0.2980 chunk 90 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 49 optimal weight: 0.0050 chunk 25 optimal weight: 0.0040 overall best weight: 0.0678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.108511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.091101 restraints weight = 22255.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.092942 restraints weight = 16938.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.094297 restraints weight = 13731.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.095082 restraints weight = 11637.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.095888 restraints weight = 10341.466| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5971 moved from start: 0.4311 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= 0.470 Angle : 0.638 22.715 15438 Z= 0.313 Chirality : 0.041 0.144 1644 Planarity : 0.003 0.023 1956 Dihedral : 3.383 16.007 1472 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % 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: -1.78 (0.21), residues: 1376 helix: 0.21 (0.43), residues: 156 sheet: -1.80 (0.32), residues: 220 loop : -1.33 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG a 294 TYR 0.017 0.001 TYR b 256 PHE 0.004 0.000 PHE a 20 TRP 0.045 0.002 TRP A 68 HIS 0.003 0.001 HIS a 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.08 (11352) covalent geometry : angle 0.51221 / 0.26 (15384) SS BOND : bond 0.19000 / 9.39 ( 27) SS BOND : angle 6.43998 / 4.02 ( 54) hydrogen bonds : bond 0.04705 / 2.85 ( 271) hydrogen bonds : angle 5.56913 / 3.91 ( 729) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1359.65 seconds wall clock time: 24 minutes 28.43 seconds (1468.43 seconds total)