Starting phenix.real_space_refine on Fri Jul 3 20:29:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vec_64997/07_2026/9vec_64997.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vec_64997/07_2026/9vec_64997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vec_64997/07_2026/9vec_64997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vec_64997/07_2026/9vec_64997.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vec_64997/07_2026/9vec_64997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vec_64997/07_2026/9vec_64997.map" } resolution = 2.7 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= 0.009 sd= 0.160 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 72 5.16 5 C 10208 2.51 5 N 2728 2.21 5 O 2864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15880 Number of models: 1 Model: "" Number of chains: 4 Chain: "K" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1080 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 32 Chain: "I" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 171 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 24} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "J" Number of atoms: 2717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2717 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 7, 'TRANS': 345} Chain breaks: 2 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 5, 'PHE:plan': 5, 'TRP:plan': 1, 'GLU:plan': 4, 'TYR:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 101 Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Restraints were copied for chains: B, E, H, C, F, L, A, D, G Time building chain proxies: 2.99, per 1000 atoms: 0.19 Number of scatterers: 15880 At special positions: 0 Unit cell: (110.245, 110.245, 125.809, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 72 16.00 O 2864 8.00 N 2728 7.00 C 10208 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 660.5 milliseconds 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3864 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 4 sheets defined 75.5% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'K' and resid 8 through 22 removed outlier: 4.208A pdb=" N GLU K 12 " --> pdb=" O GLU K 8 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 39 Processing helix chain 'K' and resid 45 through 54 Processing helix chain 'K' and resid 65 through 74 Processing helix chain 'K' and resid 79 through 92 Processing helix chain 'K' and resid 103 through 113 Processing helix chain 'K' and resid 118 through 127 Processing helix chain 'K' and resid 139 through 149 removed outlier: 3.775A pdb=" N LYS K 149 " --> pdb=" O MET K 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 65 removed outlier: 4.195A pdb=" N PHE I 54 " --> pdb=" O VAL I 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 115 Processing helix chain 'J' and resid 121 through 143 Processing helix chain 'J' and resid 168 through 178 Processing helix chain 'J' and resid 179 through 181 No H-bonds generated for 'chain 'J' and resid 179 through 181' Processing helix chain 'J' and resid 185 through 195 Processing helix chain 'J' and resid 196 through 216 Processing helix chain 'J' and resid 224 through 229 Processing helix chain 'J' and resid 229 through 237 removed outlier: 3.694A pdb=" N ILE J 235 " --> pdb=" O ARG J 231 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 241 removed outlier: 3.610A pdb=" N VAL J 241 " --> pdb=" O MET J 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 238 through 241' Processing helix chain 'J' and resid 245 through 258 Processing helix chain 'J' and resid 258 through 285 Processing helix chain 'J' and resid 298 through 311 removed outlier: 3.700A pdb=" N ALA J 302 " --> pdb=" O SER J 298 " (cutoff:3.500A) Processing helix chain 'J' and resid 322 through 358 removed outlier: 3.609A pdb=" N VAL J 334 " --> pdb=" O SER J 330 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE J 335 " --> pdb=" O CYS J 331 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N SER J 338 " --> pdb=" O VAL J 334 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE J 339 " --> pdb=" O PHE J 335 " (cutoff:3.500A) Proline residue: J 343 - end of helix Processing helix chain 'J' and resid 363 through 366 Processing helix chain 'J' and resid 367 through 384 Processing helix chain 'J' and resid 391 through 396 removed outlier: 3.835A pdb=" N ILE J 394 " --> pdb=" O THR J 391 " (cutoff:3.500A) Processing helix chain 'J' and resid 507 through 533 removed outlier: 3.504A pdb=" N ARG J 533 " --> pdb=" O PHE J 529 " (cutoff:3.500A) Processing helix chain 'J' and resid 537 through 568 removed outlier: 3.693A pdb=" N VAL J 541 " --> pdb=" O ASP J 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 22 removed outlier: 4.209A pdb=" N GLU B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 39 Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 65 through 74 Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 103 through 113 Processing helix chain 'B' and resid 118 through 127 Processing helix chain 'B' and resid 139 through 149 removed outlier: 3.775A pdb=" N LYS B 149 " --> pdb=" O MET B 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 22 removed outlier: 4.208A pdb=" N GLU E 12 " --> pdb=" O GLU E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 39 Processing helix chain 'E' and resid 45 through 54 Processing helix chain 'E' and resid 65 through 74 Processing helix chain 'E' and resid 79 through 92 Processing helix chain 'E' and resid 103 through 113 Processing helix chain 'E' and resid 118 through 127 Processing helix chain 'E' and resid 139 through 149 removed outlier: 3.774A pdb=" N LYS E 149 " --> pdb=" O MET E 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 22 removed outlier: 4.208A pdb=" N GLU H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 39 Processing helix chain 'H' and resid 45 through 54 Processing helix chain 'H' and resid 65 through 74 Processing helix chain 'H' and resid 79 through 92 Processing helix chain 'H' and resid 103 through 113 Processing helix chain 'H' and resid 118 through 127 Processing helix chain 'H' and resid 139 through 149 removed outlier: 3.774A pdb=" N LYS H 149 " --> pdb=" O MET H 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 65 removed outlier: 4.196A pdb=" N PHE C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 65 removed outlier: 4.195A pdb=" N PHE F 54 " --> pdb=" O VAL F 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 65 removed outlier: 4.195A pdb=" N PHE L 54 " --> pdb=" O VAL L 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 115 Processing helix chain 'A' and resid 121 through 143 Processing helix chain 'A' and resid 168 through 178 Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 185 through 195 Processing helix chain 'A' and resid 196 through 216 Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.694A pdb=" N ILE A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 241 removed outlier: 3.610A pdb=" N VAL A 241 " --> pdb=" O MET A 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 238 through 241' Processing helix chain 'A' and resid 245 through 258 Processing helix chain 'A' and resid 258 through 285 Processing helix chain 'A' and resid 298 through 311 removed outlier: 3.700A pdb=" N ALA A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 358 removed outlier: 3.609A pdb=" N VAL A 334 " --> pdb=" O SER A 330 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE A 335 " --> pdb=" O CYS A 331 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N SER A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 363 through 366 Processing helix chain 'A' and resid 367 through 384 Processing helix chain 'A' and resid 391 through 396 removed outlier: 3.835A pdb=" N ILE A 394 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 533 removed outlier: 3.504A pdb=" N ARG A 533 " --> pdb=" O PHE A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 568 removed outlier: 3.693A pdb=" N VAL A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 115 Processing helix chain 'D' and resid 121 through 143 Processing helix chain 'D' and resid 168 through 178 Processing helix chain 'D' and resid 179 through 181 No H-bonds generated for 'chain 'D' and resid 179 through 181' Processing helix chain 'D' and resid 185 through 195 Processing helix chain 'D' and resid 196 through 216 Processing helix chain 'D' and resid 224 through 229 Processing helix chain 'D' and resid 229 through 237 removed outlier: 3.694A pdb=" N ILE D 235 " --> pdb=" O ARG D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 241 removed outlier: 3.610A pdb=" N VAL D 241 " --> pdb=" O MET D 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 238 through 241' Processing helix chain 'D' and resid 245 through 258 Processing helix chain 'D' and resid 258 through 285 Processing helix chain 'D' and resid 298 through 311 removed outlier: 3.699A pdb=" N ALA D 302 " --> pdb=" O SER D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 358 removed outlier: 3.609A pdb=" N VAL D 334 " --> pdb=" O SER D 330 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE D 335 " --> pdb=" O CYS D 331 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N SER D 338 " --> pdb=" O VAL D 334 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE D 339 " --> pdb=" O PHE D 335 " (cutoff:3.500A) Proline residue: D 343 - end of helix Processing helix chain 'D' and resid 363 through 366 Processing helix chain 'D' and resid 367 through 384 Processing helix chain 'D' and resid 391 through 396 removed outlier: 3.835A pdb=" N ILE D 394 " --> pdb=" O THR D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 533 removed outlier: 3.504A pdb=" N ARG D 533 " --> pdb=" O PHE D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 568 removed outlier: 3.693A pdb=" N VAL D 541 " --> pdb=" O ASP D 537 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 115 Processing helix chain 'G' and resid 121 through 143 Processing helix chain 'G' and resid 168 through 178 Processing helix chain 'G' and resid 179 through 181 No H-bonds generated for 'chain 'G' and resid 179 through 181' Processing helix chain 'G' and resid 185 through 195 Processing helix chain 'G' and resid 196 through 216 Processing helix chain 'G' and resid 224 through 229 Processing helix chain 'G' and resid 229 through 237 removed outlier: 3.694A pdb=" N ILE G 235 " --> pdb=" O ARG G 231 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 241 removed outlier: 3.610A pdb=" N VAL G 241 " --> pdb=" O MET G 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 238 through 241' Processing helix chain 'G' and resid 245 through 258 Processing helix chain 'G' and resid 258 through 285 Processing helix chain 'G' and resid 298 through 311 removed outlier: 3.700A pdb=" N ALA G 302 " --> pdb=" O SER G 298 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 358 removed outlier: 3.608A pdb=" N VAL G 334 " --> pdb=" O SER G 330 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N PHE G 335 " --> pdb=" O CYS G 331 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER G 338 " --> pdb=" O VAL G 334 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE G 339 " --> pdb=" O PHE G 335 " (cutoff:3.500A) Proline residue: G 343 - end of helix Processing helix chain 'G' and resid 363 through 366 Processing helix chain 'G' and resid 367 through 384 Processing helix chain 'G' and resid 391 through 396 removed outlier: 3.835A pdb=" N ILE G 394 " --> pdb=" O THR G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 507 through 533 removed outlier: 3.503A pdb=" N ARG G 533 " --> pdb=" O PHE G 529 " (cutoff:3.500A) Processing helix chain 'G' and resid 537 through 568 removed outlier: 3.692A pdb=" N VAL G 541 " --> pdb=" O ASP G 537 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 100 through 102 Processing sheet with id=AA2, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AA3, first strand: chain 'E' and resid 100 through 102 Processing sheet with id=AA4, first strand: chain 'H' and resid 100 through 102 1104 hydrogen bonds defined for protein. 3276 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5176 1.34 - 1.46: 3805 1.46 - 1.58: 7075 1.58 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 16176 Sorted by residual: bond pdb=" CB ILE A 313 " pdb=" CG2 ILE A 313 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.86e+00 bond pdb=" CB ILE D 313 " pdb=" CG2 ILE D 313 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.84e+00 bond pdb=" CB ILE G 313 " pdb=" CG2 ILE G 313 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.82e+00 bond pdb=" CB ILE J 313 " pdb=" CG2 ILE J 313 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.79e+00 bond pdb=" CG LEU D 342 " pdb=" CD1 LEU D 342 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.29e+00 ... (remaining 16171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 21682 2.27 - 4.54: 214 4.54 - 6.81: 28 6.81 - 9.07: 4 9.07 - 11.34: 4 Bond angle restraints: 21932 Sorted by residual: angle pdb=" N VAL G 124 " pdb=" CA VAL G 124 " pdb=" C VAL G 124 " ideal model delta sigma weight residual 112.35 106.37 5.98 1.41e+00 5.03e-01 1.80e+01 angle pdb=" N VAL D 124 " pdb=" CA VAL D 124 " pdb=" C VAL D 124 " ideal model delta sigma weight residual 112.35 106.40 5.95 1.41e+00 5.03e-01 1.78e+01 angle pdb=" N VAL J 124 " pdb=" CA VAL J 124 " pdb=" C VAL J 124 " ideal model delta sigma weight residual 112.35 106.43 5.92 1.41e+00 5.03e-01 1.76e+01 angle pdb=" N VAL A 124 " pdb=" CA VAL A 124 " pdb=" C VAL A 124 " ideal model delta sigma weight residual 112.35 106.45 5.90 1.41e+00 5.03e-01 1.75e+01 angle pdb=" CB LEU F 45 " pdb=" CG LEU F 45 " pdb=" CD1 LEU F 45 " ideal model delta sigma weight residual 110.70 122.04 -11.34 3.00e+00 1.11e-01 1.43e+01 ... (remaining 21927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 8622 17.24 - 34.48: 671 34.48 - 51.72: 103 51.72 - 68.96: 20 68.96 - 86.20: 32 Dihedral angle restraints: 9448 sinusoidal: 3448 harmonic: 6000 Sorted by residual: dihedral pdb=" CA PHE D 157 " pdb=" C PHE D 157 " pdb=" N TRP D 158 " pdb=" CA TRP D 158 " ideal model delta harmonic sigma weight residual 180.00 151.62 28.38 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA PHE J 157 " pdb=" C PHE J 157 " pdb=" N TRP J 158 " pdb=" CA TRP J 158 " ideal model delta harmonic sigma weight residual 180.00 151.62 28.38 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA PHE A 157 " pdb=" C PHE A 157 " pdb=" N TRP A 158 " pdb=" CA TRP A 158 " ideal model delta harmonic sigma weight residual 180.00 151.65 28.35 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 9445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.286: 2524 0.286 - 0.573: 4 0.573 - 0.859: 0 0.859 - 1.145: 0 1.145 - 1.431: 4 Chirality restraints: 2532 Sorted by residual: chirality pdb=" CG LEU L 45 " pdb=" CB LEU L 45 " pdb=" CD1 LEU L 45 " pdb=" CD2 LEU L 45 " both_signs ideal model delta sigma weight residual False -2.59 -1.16 -1.43 2.00e-01 2.50e+01 5.12e+01 chirality pdb=" CG LEU C 45 " pdb=" CB LEU C 45 " pdb=" CD1 LEU C 45 " pdb=" CD2 LEU C 45 " both_signs ideal model delta sigma weight residual False -2.59 -1.16 -1.43 2.00e-01 2.50e+01 5.12e+01 chirality pdb=" CG LEU I 45 " pdb=" CB LEU I 45 " pdb=" CD1 LEU I 45 " pdb=" CD2 LEU I 45 " both_signs ideal model delta sigma weight residual False -2.59 -1.16 -1.43 2.00e-01 2.50e+01 5.12e+01 ... (remaining 2529 not shown) Planarity restraints: 2780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 227 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.89e+00 pdb=" C ILE A 227 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE A 227 " -0.014 2.00e-02 2.50e+03 pdb=" N ARG A 228 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE J 227 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.84e+00 pdb=" C ILE J 227 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE J 227 " -0.014 2.00e-02 2.50e+03 pdb=" N ARG J 228 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 227 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.81e+00 pdb=" C ILE D 227 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE D 227 " -0.014 2.00e-02 2.50e+03 pdb=" N ARG D 228 " -0.013 2.00e-02 2.50e+03 ... (remaining 2777 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 255 2.65 - 3.21: 16051 3.21 - 3.78: 25087 3.78 - 4.34: 35219 4.34 - 4.90: 57388 Nonbonded interactions: 134000 Sorted by model distance: nonbonded pdb=" O THR A 311 " pdb=" OG1 THR A 312 " model vdw 2.089 3.040 nonbonded pdb=" O THR G 311 " pdb=" OG1 THR G 312 " model vdw 2.090 3.040 nonbonded pdb=" O THR J 311 " pdb=" OG1 THR J 312 " model vdw 2.090 3.040 nonbonded pdb=" O THR D 311 " pdb=" OG1 THR D 312 " model vdw 2.091 3.040 nonbonded pdb=" OE1 GLU K 84 " pdb=" NH1 ARG K 87 " model vdw 2.107 3.120 ... (remaining 133995 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 'K' selection = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'C' selection = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'A' selection = chain 'D' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 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: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 13.710 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 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 0.065 16176 Z= 0.392 Angle : 0.661 11.342 21932 Z= 0.367 Chirality : 0.077 1.431 2532 Planarity : 0.004 0.033 2780 Dihedral : 13.625 86.204 5584 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.16), residues: 2048 helix: -0.94 (0.12), residues: 1528 sheet: None (None), residues: 0 loop : -2.26 (0.22), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 511 TYR 0.018 0.002 TYR A 545 PHE 0.014 0.002 PHE E 69 TRP 0.012 0.002 TRP G 379 HIS 0.003 0.001 HIS G 258 Details of bonding type rmsd/Z covalent geometry : bond 0.01003 / 0.39 (16176) covalent geometry : angle 0.66081 / 0.37 (21932) hydrogen bonds : bond 0.13827 / 9.49 ( 1104) hydrogen bonds : angle 6.08396 / 4.43 ( 3276) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: K 37 MET cc_start: 0.8197 (mtp) cc_final: 0.7830 (mtp) REVERT: K 38 ARG cc_start: 0.7854 (mtm-85) cc_final: 0.7579 (ttp-170) REVERT: J 167 PHE cc_start: 0.7954 (m-10) cc_final: 0.7733 (m-80) REVERT: B 37 MET cc_start: 0.8162 (mtp) cc_final: 0.7818 (mtp) REVERT: B 38 ARG cc_start: 0.7918 (mtm-85) cc_final: 0.7700 (ttp-170) REVERT: E 37 MET cc_start: 0.8161 (mtp) cc_final: 0.7840 (mtp) REVERT: H 37 MET cc_start: 0.8198 (mtp) cc_final: 0.7904 (mtp) REVERT: A 167 PHE cc_start: 0.8018 (m-10) cc_final: 0.7702 (m-80) REVERT: D 167 PHE cc_start: 0.7885 (m-10) cc_final: 0.7610 (m-80) REVERT: D 243 ARG cc_start: 0.7365 (tpp-160) cc_final: 0.7113 (tpp-160) REVERT: D 553 MET cc_start: 0.8439 (mmm) cc_final: 0.8185 (mmm) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.7327 time to fit residues: 230.4851 Evaluate side-chains 214 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.0170 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 54 ASN J 112 ASN J 260 GLN J 544 GLN B 54 ASN E 54 ASN H 54 ASN A 147 GLN A 544 GLN A 560 GLN D 147 GLN D 544 GLN D 560 GLN G 112 ASN G 544 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.177790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.143719 restraints weight = 16546.103| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.22 r_work: 0.3276 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16176 Z= 0.125 Angle : 0.489 5.896 21932 Z= 0.269 Chirality : 0.038 0.159 2532 Planarity : 0.004 0.039 2780 Dihedral : 4.033 26.444 2244 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.15 % Allowed : 9.04 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.18), residues: 2048 helix: 0.85 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -1.63 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 562 TYR 0.014 0.001 TYR G 125 PHE 0.012 0.001 PHE H 66 TRP 0.019 0.002 TRP A 379 HIS 0.002 0.000 HIS A 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (16176) covalent geometry : angle 0.48912 / 0.27 (21932) hydrogen bonds : bond 0.04027 / 2.65 ( 1104) hydrogen bonds : angle 4.18403 / 3.05 ( 3276) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 245 time to evaluate : 0.650 Fit side-chains REVERT: K 15 GLU cc_start: 0.7041 (tp30) cc_final: 0.6721 (tp30) REVERT: K 37 MET cc_start: 0.8784 (mtp) cc_final: 0.8339 (mtp) REVERT: J 112 ASN cc_start: 0.7850 (m-40) cc_final: 0.7564 (m110) REVERT: J 295 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8380 (mt-10) REVERT: B 15 GLU cc_start: 0.7119 (tp30) cc_final: 0.6807 (tp30) REVERT: B 37 MET cc_start: 0.8798 (mtp) cc_final: 0.8440 (mtp) REVERT: B 70 LEU cc_start: 0.8255 (mt) cc_final: 0.8001 (mm) REVERT: E 15 GLU cc_start: 0.6926 (tp30) cc_final: 0.6686 (tp30) REVERT: E 37 MET cc_start: 0.8777 (mtp) cc_final: 0.8373 (mtp) REVERT: E 38 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7643 (mtp180) REVERT: E 43 ASN cc_start: 0.8388 (t0) cc_final: 0.7806 (p0) REVERT: H 15 GLU cc_start: 0.7073 (tp30) cc_final: 0.6738 (tp30) REVERT: H 37 MET cc_start: 0.8770 (mtp) cc_final: 0.8419 (mtp) REVERT: H 38 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7750 (mtp180) REVERT: A 188 TRP cc_start: 0.6723 (m100) cc_final: 0.6467 (m-90) REVERT: A 395 TYR cc_start: 0.8322 (m-80) cc_final: 0.8040 (m-80) REVERT: A 560 GLN cc_start: 0.7839 (tp40) cc_final: 0.7223 (tp-100) REVERT: D 188 TRP cc_start: 0.6568 (m100) cc_final: 0.6282 (m-90) REVERT: D 354 LYS cc_start: 0.8991 (tttp) cc_final: 0.8739 (ttpp) REVERT: D 395 TYR cc_start: 0.8374 (m-80) cc_final: 0.8099 (m-80) REVERT: D 539 ARG cc_start: 0.8399 (mtt180) cc_final: 0.8118 (ttm-80) REVERT: D 553 MET cc_start: 0.9495 (mmm) cc_final: 0.9032 (mmm) REVERT: D 555 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7486 (mmt180) REVERT: D 560 GLN cc_start: 0.7964 (tp40) cc_final: 0.7430 (tp-100) REVERT: D 562 ARG cc_start: 0.7577 (ttm-80) cc_final: 0.7337 (ttm-80) REVERT: G 106 VAL cc_start: 0.7050 (t) cc_final: 0.6793 (p) REVERT: G 188 TRP cc_start: 0.6087 (m-10) cc_final: 0.5856 (m100) REVERT: G 295 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8310 (mt-10) REVERT: G 560 GLN cc_start: 0.7532 (tt0) cc_final: 0.7250 (tt0) outliers start: 18 outliers final: 7 residues processed: 252 average time/residue: 0.7214 time to fit residues: 197.2106 Evaluate side-chains 228 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 218 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain D residue 555 ARG Chi-restraints excluded: chain G residue 555 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 30 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 138 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 54 ASN J 357 GLN B 54 ASN E 54 ASN H 54 ASN A 147 GLN A 260 GLN A 357 GLN D 260 GLN D 357 GLN G 112 ASN G 260 GLN G 357 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.173917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.140152 restraints weight = 16793.329| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.95 r_work: 0.3219 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16176 Z= 0.146 Angle : 0.504 6.341 21932 Z= 0.272 Chirality : 0.039 0.159 2532 Planarity : 0.004 0.038 2780 Dihedral : 3.863 22.918 2244 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.05 % Allowed : 11.47 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.18), residues: 2048 helix: 1.14 (0.13), residues: 1568 sheet: None (None), residues: 0 loop : -1.18 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 562 TYR 0.016 0.002 TYR G 545 PHE 0.014 0.002 PHE A 340 TRP 0.018 0.002 TRP G 379 HIS 0.002 0.001 HIS A 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (16176) covalent geometry : angle 0.50442 / 0.27 (21932) hydrogen bonds : bond 0.04432 / 2.95 ( 1104) hydrogen bonds : angle 4.10786 / 2.99 ( 3276) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 226 time to evaluate : 0.740 Fit side-chains REVERT: K 37 MET cc_start: 0.8795 (mtp) cc_final: 0.8436 (mtp) REVERT: K 38 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7806 (mtp180) REVERT: K 144 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.7498 (mp10) REVERT: J 112 ASN cc_start: 0.8015 (m-40) cc_final: 0.7709 (m110) REVERT: J 125 TYR cc_start: 0.6144 (t80) cc_final: 0.5939 (t80) REVERT: B 15 GLU cc_start: 0.7299 (tp30) cc_final: 0.7085 (tp30) REVERT: B 37 MET cc_start: 0.8806 (mtp) cc_final: 0.8448 (mtp) REVERT: B 38 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7805 (mtp180) REVERT: B 120 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8201 (mt-10) REVERT: B 144 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.7499 (mp10) REVERT: E 37 MET cc_start: 0.8795 (mtp) cc_final: 0.8454 (mtp) REVERT: E 38 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.7859 (mtp180) REVERT: H 37 MET cc_start: 0.8792 (mtp) cc_final: 0.8448 (mtp) REVERT: H 38 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7731 (mtp180) REVERT: H 120 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8203 (mt-10) REVERT: A 112 ASN cc_start: 0.7974 (m110) cc_final: 0.7767 (m-40) REVERT: A 188 TRP cc_start: 0.6788 (m100) cc_final: 0.6574 (m-90) REVERT: D 188 TRP cc_start: 0.6783 (m100) cc_final: 0.6555 (m-90) REVERT: D 354 LYS cc_start: 0.9090 (tttp) cc_final: 0.8872 (ttpp) REVERT: D 395 TYR cc_start: 0.8235 (m-80) cc_final: 0.7997 (m-80) REVERT: D 539 ARG cc_start: 0.8474 (mtt180) cc_final: 0.8186 (mtm-85) REVERT: D 553 MET cc_start: 0.9408 (mmm) cc_final: 0.9113 (mmm) REVERT: D 560 GLN cc_start: 0.7891 (tp40) cc_final: 0.7379 (tp-100) REVERT: D 562 ARG cc_start: 0.7695 (ttm-80) cc_final: 0.7449 (ttm-80) REVERT: G 112 ASN cc_start: 0.7761 (m-40) cc_final: 0.7503 (m110) REVERT: G 125 TYR cc_start: 0.6325 (t80) cc_final: 0.5896 (t80) REVERT: G 170 GLU cc_start: 0.7384 (tt0) cc_final: 0.7151 (tt0) REVERT: G 188 TRP cc_start: 0.6178 (m-10) cc_final: 0.5948 (m100) REVERT: G 560 GLN cc_start: 0.7503 (tt0) cc_final: 0.7196 (tt0) outliers start: 32 outliers final: 13 residues processed: 245 average time/residue: 0.6053 time to fit residues: 162.2216 Evaluate side-chains 228 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 209 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 72 MET Chi-restraints excluded: chain K residue 144 GLN Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain G residue 555 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 162 optimal weight: 0.5980 chunk 93 optimal weight: 0.3980 chunk 85 optimal weight: 0.7980 chunk 103 optimal weight: 50.0000 chunk 76 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 54 ASN J 260 GLN J 357 GLN B 54 ASN E 54 ASN H 54 ASN A 260 GLN A 357 GLN D 147 GLN D 260 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.175728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.141011 restraints weight = 16705.098| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.92 r_work: 0.3255 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16176 Z= 0.113 Angle : 0.470 8.190 21932 Z= 0.246 Chirality : 0.037 0.158 2532 Planarity : 0.003 0.035 2780 Dihedral : 3.571 21.044 2244 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.44 % Allowed : 12.88 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.18), residues: 2048 helix: 1.68 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.96 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 562 TYR 0.013 0.001 TYR D 545 PHE 0.015 0.001 PHE A 332 TRP 0.015 0.001 TRP J 379 HIS 0.001 0.000 HIS J 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (16176) covalent geometry : angle 0.46958 / 0.25 (21932) hydrogen bonds : bond 0.03729 / 2.47 ( 1104) hydrogen bonds : angle 3.82379 / 2.79 ( 3276) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 236 time to evaluate : 0.598 Fit side-chains REVERT: K 37 MET cc_start: 0.8771 (mtp) cc_final: 0.8401 (mtp) REVERT: K 38 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7804 (mtp180) REVERT: J 112 ASN cc_start: 0.7784 (m-40) cc_final: 0.7378 (m110) REVERT: B 37 MET cc_start: 0.8805 (mtp) cc_final: 0.8437 (mtp) REVERT: B 38 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7805 (mtp180) REVERT: E 37 MET cc_start: 0.8785 (mtp) cc_final: 0.8413 (mtp) REVERT: E 38 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7781 (mtp180) REVERT: E 65 ASP cc_start: 0.8115 (p0) cc_final: 0.7870 (p0) REVERT: H 37 MET cc_start: 0.8785 (mtp) cc_final: 0.8414 (mtp) REVERT: H 38 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7734 (mtp180) REVERT: H 70 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7971 (mm) REVERT: A 395 TYR cc_start: 0.8204 (m-80) cc_final: 0.7979 (m-80) REVERT: A 560 GLN cc_start: 0.7876 (tp40) cc_final: 0.7193 (tp-100) REVERT: D 354 LYS cc_start: 0.9042 (tttp) cc_final: 0.8780 (ttpp) REVERT: D 395 TYR cc_start: 0.8290 (m-80) cc_final: 0.8023 (m-80) REVERT: D 539 ARG cc_start: 0.8511 (mtt180) cc_final: 0.8235 (mtm-85) REVERT: D 553 MET cc_start: 0.9425 (mmm) cc_final: 0.9087 (mmm) REVERT: D 555 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7475 (mmt180) REVERT: D 560 GLN cc_start: 0.7871 (tp40) cc_final: 0.7336 (tp-100) REVERT: G 112 ASN cc_start: 0.7804 (m-40) cc_final: 0.7467 (m110) REVERT: G 115 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7781 (mm-30) REVERT: G 233 LEU cc_start: 0.6998 (mt) cc_final: 0.6780 (mp) REVERT: G 560 GLN cc_start: 0.7538 (tt0) cc_final: 0.7226 (tt0) outliers start: 38 outliers final: 12 residues processed: 263 average time/residue: 0.6286 time to fit residues: 180.4348 Evaluate side-chains 235 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 217 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 72 MET Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 555 ARG Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 555 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 141 optimal weight: 0.6980 chunk 189 optimal weight: 0.0170 chunk 79 optimal weight: 10.0000 chunk 166 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 174 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 54 ASN J 260 GLN J 357 GLN B 54 ASN E 54 ASN H 54 ASN A 260 GLN A 357 GLN D 260 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.175742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.139904 restraints weight = 16821.394| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.10 r_work: 0.3250 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16176 Z= 0.105 Angle : 0.459 9.519 21932 Z= 0.239 Chirality : 0.037 0.180 2532 Planarity : 0.003 0.033 2780 Dihedral : 3.389 17.329 2244 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.18 % Allowed : 14.42 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.19), residues: 2048 helix: 1.91 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.78 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 174 TYR 0.012 0.001 TYR D 545 PHE 0.012 0.001 PHE A 332 TRP 0.013 0.001 TRP G 379 HIS 0.002 0.001 HIS J 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (16176) covalent geometry : angle 0.45932 / 0.24 (21932) hydrogen bonds : bond 0.03560 / 2.36 ( 1104) hydrogen bonds : angle 3.73714 / 2.74 ( 3276) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 227 time to evaluate : 0.607 Fit side-chains REVERT: K 15 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6816 (tm-30) REVERT: K 37 MET cc_start: 0.8743 (mtp) cc_final: 0.8361 (mtp) REVERT: K 38 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7738 (mtp180) REVERT: J 112 ASN cc_start: 0.7674 (m-40) cc_final: 0.7263 (m-40) REVERT: J 555 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7657 (mtt-85) REVERT: B 37 MET cc_start: 0.8784 (mtp) cc_final: 0.8400 (mtp) REVERT: B 38 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7735 (mtp180) REVERT: B 120 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8083 (mt-10) REVERT: E 38 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7751 (mtp180) REVERT: E 65 ASP cc_start: 0.8047 (p0) cc_final: 0.7778 (p0) REVERT: H 37 MET cc_start: 0.8753 (mtp) cc_final: 0.8367 (mtp) REVERT: H 38 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7669 (mtp180) REVERT: H 120 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8080 (mt-10) REVERT: A 395 TYR cc_start: 0.8268 (m-80) cc_final: 0.8006 (m-80) REVERT: D 354 LYS cc_start: 0.9039 (tttp) cc_final: 0.8750 (ttpp) REVERT: D 395 TYR cc_start: 0.8255 (m-80) cc_final: 0.7949 (m-80) REVERT: D 539 ARG cc_start: 0.8455 (mtt180) cc_final: 0.8188 (mtm-85) REVERT: D 553 MET cc_start: 0.9446 (mmm) cc_final: 0.9087 (mmm) REVERT: D 555 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7475 (mmt180) REVERT: D 560 GLN cc_start: 0.7928 (tp40) cc_final: 0.7368 (tp-100) REVERT: D 562 ARG cc_start: 0.7594 (ttm-80) cc_final: 0.7287 (ttm-80) REVERT: G 112 ASN cc_start: 0.7754 (m-40) cc_final: 0.7412 (m110) REVERT: G 233 LEU cc_start: 0.6865 (mt) cc_final: 0.6638 (mp) REVERT: G 560 GLN cc_start: 0.7513 (tt0) cc_final: 0.7019 (tt0) outliers start: 34 outliers final: 15 residues processed: 244 average time/residue: 0.6794 time to fit residues: 180.8406 Evaluate side-chains 242 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 220 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 15 GLU Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 72 MET Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 555 ARG Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain H residue 10 ILE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 555 ARG Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 555 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 63 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 54 ASN J 260 GLN J 357 GLN B 54 ASN E 54 ASN H 54 ASN A 260 GLN A 357 GLN D 260 GLN D 357 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.171386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.136284 restraints weight = 16889.958| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.84 r_work: 0.3206 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16176 Z= 0.171 Angle : 0.534 8.392 21932 Z= 0.278 Chirality : 0.041 0.252 2532 Planarity : 0.004 0.037 2780 Dihedral : 3.680 17.550 2244 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.56 % Allowed : 14.81 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.18), residues: 2048 helix: 1.57 (0.13), residues: 1552 sheet: None (None), residues: 0 loop : -0.72 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 562 TYR 0.018 0.002 TYR G 545 PHE 0.016 0.002 PHE A 340 TRP 0.013 0.002 TRP J 379 HIS 0.002 0.001 HIS G 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 (16176) covalent geometry : angle 0.53353 / 0.28 (21932) hydrogen bonds : bond 0.04544 / 3.03 ( 1104) hydrogen bonds : angle 4.00522 / 2.92 ( 3276) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 230 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: K 37 MET cc_start: 0.8752 (mtp) cc_final: 0.8362 (mtp) REVERT: K 38 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7813 (mtp180) REVERT: K 120 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8077 (mt-10) REVERT: K 144 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.7373 (mp10) REVERT: J 112 ASN cc_start: 0.7773 (m-40) cc_final: 0.7462 (m-40) REVERT: J 555 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7659 (mtt-85) REVERT: B 37 MET cc_start: 0.8795 (mtp) cc_final: 0.8409 (mtp) REVERT: B 38 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7814 (mtp180) REVERT: B 120 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8067 (mt-10) REVERT: B 144 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7374 (mp10) REVERT: E 15 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6681 (tp30) REVERT: E 37 MET cc_start: 0.8707 (mtp) cc_final: 0.8372 (mtp) REVERT: E 38 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7725 (mtp180) REVERT: E 144 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7365 (mp10) REVERT: H 37 MET cc_start: 0.8772 (mtp) cc_final: 0.8381 (mtp) REVERT: H 38 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7742 (mtp180) REVERT: H 144 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.7383 (mp10) REVERT: A 112 ASN cc_start: 0.7698 (m110) cc_final: 0.7488 (m-40) REVERT: A 555 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7754 (mmt180) REVERT: D 354 LYS cc_start: 0.9064 (tttp) cc_final: 0.8785 (ttpp) REVERT: D 395 TYR cc_start: 0.8202 (m-80) cc_final: 0.7968 (m-80) REVERT: D 539 ARG cc_start: 0.8447 (mtt180) cc_final: 0.8217 (mtm-85) REVERT: D 553 MET cc_start: 0.9295 (mmm) cc_final: 0.9025 (mmm) REVERT: D 555 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7619 (mmt180) REVERT: D 560 GLN cc_start: 0.7910 (tp40) cc_final: 0.7312 (tp-100) REVERT: D 562 ARG cc_start: 0.7650 (ttm-80) cc_final: 0.7384 (ttm-80) REVERT: G 112 ASN cc_start: 0.7858 (m-40) cc_final: 0.7630 (m110) REVERT: G 188 TRP cc_start: 0.6351 (m-10) cc_final: 0.6128 (m100) REVERT: G 560 GLN cc_start: 0.7701 (tt0) cc_final: 0.6983 (mt0) outliers start: 40 outliers final: 16 residues processed: 249 average time/residue: 0.6596 time to fit residues: 179.1498 Evaluate side-chains 250 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 ILE Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 72 MET Chi-restraints excluded: chain K residue 144 GLN Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 555 ARG Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 144 GLN Chi-restraints excluded: chain H residue 10 ILE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 144 GLN Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 555 ARG Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 555 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 131 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 54 ASN J 260 GLN J 357 GLN B 54 ASN E 54 ASN H 54 ASN A 260 GLN A 357 GLN D 260 GLN D 357 GLN G 260 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.171231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.125109 restraints weight = 17308.639| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.92 r_work: 0.3192 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16176 Z= 0.155 Angle : 0.515 8.050 21932 Z= 0.268 Chirality : 0.040 0.268 2532 Planarity : 0.003 0.037 2780 Dihedral : 3.639 18.223 2244 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.82 % Allowed : 15.26 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.18), residues: 2048 helix: 1.57 (0.13), residues: 1552 sheet: None (None), residues: 0 loop : -0.67 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 562 TYR 0.017 0.002 TYR G 545 PHE 0.013 0.002 PHE J 340 TRP 0.014 0.002 TRP D 379 HIS 0.002 0.001 HIS G 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (16176) covalent geometry : angle 0.51525 / 0.27 (21932) hydrogen bonds : bond 0.04259 / 2.84 ( 1104) hydrogen bonds : angle 3.93958 / 2.87 ( 3276) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 234 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 37 MET cc_start: 0.8699 (mtp) cc_final: 0.8311 (mtp) REVERT: K 38 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7711 (mtp180) REVERT: K 120 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8096 (mt-10) REVERT: K 144 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7148 (mp10) REVERT: J 112 ASN cc_start: 0.7616 (m-40) cc_final: 0.7387 (m110) REVERT: J 555 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7566 (mtt-85) REVERT: B 15 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6863 (tp30) REVERT: B 37 MET cc_start: 0.8750 (mtp) cc_final: 0.8366 (mtp) REVERT: B 38 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7602 (mtp180) REVERT: E 37 MET cc_start: 0.8668 (mtp) cc_final: 0.8321 (mtp) REVERT: E 38 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.7675 (mtp180) REVERT: E 65 ASP cc_start: 0.7921 (p0) cc_final: 0.7659 (p0) REVERT: H 37 MET cc_start: 0.8756 (mtp) cc_final: 0.8378 (mtp) REVERT: H 38 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7585 (mtp180) REVERT: H 144 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7187 (mp10) REVERT: A 555 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7612 (mmt180) REVERT: A 560 GLN cc_start: 0.7942 (tp40) cc_final: 0.7187 (tp-100) REVERT: D 354 LYS cc_start: 0.9051 (tttp) cc_final: 0.8725 (ttpp) REVERT: D 395 TYR cc_start: 0.8161 (m-80) cc_final: 0.7912 (m-80) REVERT: D 539 ARG cc_start: 0.8421 (mtt180) cc_final: 0.8194 (mtm-85) REVERT: D 553 MET cc_start: 0.9304 (mmm) cc_final: 0.9084 (mmm) REVERT: D 555 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7551 (mmt180) REVERT: D 560 GLN cc_start: 0.7858 (tp40) cc_final: 0.7253 (tp-100) REVERT: D 562 ARG cc_start: 0.7613 (ttm-80) cc_final: 0.7370 (ttp-170) REVERT: G 112 ASN cc_start: 0.7688 (m-40) cc_final: 0.7405 (m110) REVERT: G 560 GLN cc_start: 0.7638 (tt0) cc_final: 0.6943 (mt0) outliers start: 44 outliers final: 18 residues processed: 256 average time/residue: 0.6973 time to fit residues: 194.3598 Evaluate side-chains 254 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 ILE Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 72 MET Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 144 GLN Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 555 ARG Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain H residue 10 ILE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 144 GLN Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 555 ARG Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 555 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 18 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 chunk 20 optimal weight: 8.9990 chunk 133 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 54 ASN J 260 GLN J 357 GLN B 54 ASN E 54 ASN H 54 ASN A 260 GLN A 357 GLN D 260 GLN D 357 GLN G 260 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.172288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.123627 restraints weight = 17625.399| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.76 r_work: 0.3222 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16176 Z= 0.127 Angle : 0.479 7.287 21932 Z= 0.251 Chirality : 0.039 0.293 2532 Planarity : 0.003 0.035 2780 Dihedral : 3.524 17.402 2244 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.08 % Allowed : 15.06 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.19), residues: 2048 helix: 1.77 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.62 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 562 TYR 0.015 0.001 TYR D 545 PHE 0.012 0.001 PHE J 332 TRP 0.014 0.001 TRP D 379 HIS 0.001 0.000 HIS D 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (16176) covalent geometry : angle 0.47902 / 0.25 (21932) hydrogen bonds : bond 0.03851 / 2.56 ( 1104) hydrogen bonds : angle 3.83221 / 2.80 ( 3276) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 223 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 15 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.7006 (tp30) REVERT: K 37 MET cc_start: 0.8673 (mtp) cc_final: 0.8292 (mtp) REVERT: K 38 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7665 (mtp180) REVERT: J 238 MET cc_start: 0.8180 (mmp) cc_final: 0.7927 (mmp) REVERT: J 239 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7813 (mt) REVERT: J 555 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7556 (mtt-85) REVERT: B 37 MET cc_start: 0.8687 (mtp) cc_final: 0.8310 (mtp) REVERT: B 38 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7608 (mtp180) REVERT: B 120 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8050 (mt-10) REVERT: E 37 MET cc_start: 0.8650 (mtp) cc_final: 0.8285 (mtp) REVERT: E 38 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7593 (mtp180) REVERT: E 65 ASP cc_start: 0.7851 (p0) cc_final: 0.7614 (p0) REVERT: H 37 MET cc_start: 0.8699 (mtp) cc_final: 0.8324 (mtp) REVERT: H 38 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7582 (mtp180) REVERT: H 120 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8090 (mt-10) REVERT: D 238 MET cc_start: 0.8092 (mmp) cc_final: 0.7764 (mmp) REVERT: D 354 LYS cc_start: 0.9006 (tttp) cc_final: 0.8674 (ttpp) REVERT: D 395 TYR cc_start: 0.8097 (m-80) cc_final: 0.7746 (m-80) REVERT: D 539 ARG cc_start: 0.8401 (mtt180) cc_final: 0.8154 (mtm-85) REVERT: D 553 MET cc_start: 0.9327 (mmm) cc_final: 0.9065 (mmm) REVERT: D 555 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7420 (mmt180) REVERT: D 560 GLN cc_start: 0.7790 (tp40) cc_final: 0.7170 (tp-100) REVERT: D 562 ARG cc_start: 0.7579 (ttm-80) cc_final: 0.7281 (ttm-80) REVERT: G 112 ASN cc_start: 0.7581 (m-40) cc_final: 0.7255 (m-40) REVERT: G 560 GLN cc_start: 0.7623 (tt0) cc_final: 0.6926 (mt0) outliers start: 48 outliers final: 17 residues processed: 249 average time/residue: 0.6513 time to fit residues: 177.3779 Evaluate side-chains 245 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 220 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 15 GLU Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 72 MET Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 555 ARG Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 555 ARG Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 555 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 197 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 180 optimal weight: 10.0000 chunk 187 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 100 optimal weight: 0.5980 chunk 165 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 54 ASN J 260 GLN J 357 GLN B 54 ASN E 54 ASN H 54 ASN A 260 GLN A 357 GLN D 260 GLN D 357 GLN G 260 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.171310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.122810 restraints weight = 17393.036| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.74 r_work: 0.3206 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16176 Z= 0.138 Angle : 0.507 11.578 21932 Z= 0.262 Chirality : 0.040 0.321 2532 Planarity : 0.003 0.036 2780 Dihedral : 3.560 17.189 2244 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.63 % Allowed : 15.64 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.19), residues: 2048 helix: 1.71 (0.13), residues: 1552 sheet: None (None), residues: 0 loop : -0.61 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 562 TYR 0.016 0.002 TYR A 545 PHE 0.014 0.001 PHE D 332 TRP 0.013 0.001 TRP G 379 HIS 0.001 0.000 HIS J 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (16176) covalent geometry : angle 0.50672 / 0.26 (21932) hydrogen bonds : bond 0.04012 / 2.67 ( 1104) hydrogen bonds : angle 3.87677 / 2.83 ( 3276) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 225 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 37 MET cc_start: 0.8532 (mtp) cc_final: 0.8135 (mtp) REVERT: K 38 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7595 (mtp180) REVERT: K 120 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7947 (mt-10) REVERT: K 144 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7047 (mp10) REVERT: J 112 ASN cc_start: 0.7421 (m110) cc_final: 0.7158 (m-40) REVERT: J 238 MET cc_start: 0.8091 (mmp) cc_final: 0.7763 (mmp) REVERT: J 555 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.7350 (mtt-85) REVERT: B 37 MET cc_start: 0.8574 (mtp) cc_final: 0.8176 (mtp) REVERT: B 38 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7470 (mtp180) REVERT: B 120 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7977 (mt-10) REVERT: E 37 MET cc_start: 0.8495 (mtp) cc_final: 0.8114 (mtp) REVERT: E 38 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7488 (mtp180) REVERT: H 37 MET cc_start: 0.8567 (mtp) cc_final: 0.8176 (mtp) REVERT: H 38 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7451 (mtp180) REVERT: H 120 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7999 (mt-10) REVERT: H 144 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7071 (mp10) REVERT: A 555 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7391 (mmt180) REVERT: A 560 GLN cc_start: 0.7703 (tp40) cc_final: 0.6879 (tp-100) REVERT: D 238 MET cc_start: 0.8033 (mmp) cc_final: 0.7673 (mmp) REVERT: D 354 LYS cc_start: 0.8948 (tttp) cc_final: 0.8587 (ttpp) REVERT: D 395 TYR cc_start: 0.7973 (m-80) cc_final: 0.7601 (m-80) REVERT: D 539 ARG cc_start: 0.8293 (mtt180) cc_final: 0.8029 (mtm-85) REVERT: D 553 MET cc_start: 0.9153 (mmm) cc_final: 0.8930 (mmm) REVERT: D 555 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.7215 (mmt180) REVERT: D 560 GLN cc_start: 0.7759 (tp40) cc_final: 0.7101 (tp-100) REVERT: G 112 ASN cc_start: 0.7447 (m-40) cc_final: 0.7151 (m-40) REVERT: G 560 GLN cc_start: 0.7506 (tt0) cc_final: 0.6816 (mt0) outliers start: 41 outliers final: 19 residues processed: 245 average time/residue: 0.7015 time to fit residues: 187.5549 Evaluate side-chains 247 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 219 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 72 MET Chi-restraints excluded: chain K residue 144 GLN Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 555 ARG Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 144 GLN Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 555 ARG Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 555 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 63 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 56 optimal weight: 0.0070 chunk 103 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 195 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 196 optimal weight: 0.7980 chunk 193 optimal weight: 1.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 54 ASN J 260 GLN J 357 GLN B 54 ASN E 54 ASN H 54 ASN A 260 GLN A 357 GLN D 260 GLN D 357 GLN G 260 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.172857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.125307 restraints weight = 17973.829| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.84 r_work: 0.3249 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16176 Z= 0.105 Angle : 0.472 11.682 21932 Z= 0.240 Chirality : 0.038 0.302 2532 Planarity : 0.003 0.038 2780 Dihedral : 3.383 16.335 2244 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.86 % Allowed : 16.67 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.19), residues: 2048 helix: 1.98 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.52 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 562 TYR 0.013 0.001 TYR D 545 PHE 0.014 0.001 PHE A 332 TRP 0.014 0.001 TRP G 379 HIS 0.001 0.000 HIS D 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (16176) covalent geometry : angle 0.47154 / 0.24 (21932) hydrogen bonds : bond 0.03413 / 2.26 ( 1104) hydrogen bonds : angle 3.73064 / 2.73 ( 3276) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 235 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 37 MET cc_start: 0.8697 (mtp) cc_final: 0.8309 (mtp) REVERT: K 38 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7693 (mtp180) REVERT: K 125 MET cc_start: 0.8888 (ttt) cc_final: 0.8516 (ttt) REVERT: J 238 MET cc_start: 0.8125 (mmp) cc_final: 0.7906 (mmp) REVERT: J 555 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7545 (mtt-85) REVERT: B 37 MET cc_start: 0.8706 (mtp) cc_final: 0.8341 (mtp) REVERT: B 38 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7666 (mtp180) REVERT: B 120 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7944 (mt-10) REVERT: E 37 MET cc_start: 0.8661 (mtp) cc_final: 0.8286 (mtp) REVERT: E 38 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7604 (mtp180) REVERT: E 65 ASP cc_start: 0.7895 (p0) cc_final: 0.7636 (p0) REVERT: H 37 MET cc_start: 0.8709 (mtp) cc_final: 0.8329 (mtp) REVERT: H 38 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7589 (mtp180) REVERT: H 120 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7976 (mt-10) REVERT: A 555 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7521 (mmt180) REVERT: A 560 GLN cc_start: 0.7863 (tp40) cc_final: 0.7142 (tp-100) REVERT: D 238 MET cc_start: 0.8049 (mmp) cc_final: 0.7685 (mmp) REVERT: D 354 LYS cc_start: 0.9098 (tttp) cc_final: 0.8776 (ttpp) REVERT: D 395 TYR cc_start: 0.8083 (m-80) cc_final: 0.7732 (m-80) REVERT: D 539 ARG cc_start: 0.8380 (mtt180) cc_final: 0.8113 (mtm-85) REVERT: D 553 MET cc_start: 0.9364 (mmm) cc_final: 0.9054 (mmm) REVERT: D 555 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7278 (mmt180) REVERT: D 560 GLN cc_start: 0.7754 (tp40) cc_final: 0.7138 (tp-100) REVERT: G 112 ASN cc_start: 0.7636 (m-40) cc_final: 0.7348 (m-40) REVERT: G 560 GLN cc_start: 0.7511 (tt0) cc_final: 0.6830 (mt0) outliers start: 29 outliers final: 13 residues processed: 249 average time/residue: 0.6873 time to fit residues: 186.2105 Evaluate side-chains 244 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 224 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 72 MET Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 555 ARG Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 555 ARG Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 555 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 56 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 54 ASN J 260 GLN J 357 GLN B 54 ASN E 54 ASN H 54 ASN A 260 GLN A 357 GLN D 260 GLN D 357 GLN G 260 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.168629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.118379 restraints weight = 17577.861| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.77 r_work: 0.3226 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16176 Z= 0.135 Angle : 0.508 11.625 21932 Z= 0.261 Chirality : 0.040 0.310 2532 Planarity : 0.003 0.050 2780 Dihedral : 3.492 16.104 2244 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.31 % Allowed : 16.54 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.19), residues: 2048 helix: 1.83 (0.13), residues: 1552 sheet: None (None), residues: 0 loop : -0.51 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 174 TYR 0.016 0.001 TYR D 545 PHE 0.014 0.001 PHE G 275 TRP 0.013 0.001 TRP G 379 HIS 0.001 0.000 HIS J 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (16176) covalent geometry : angle 0.50753 / 0.26 (21932) hydrogen bonds : bond 0.03905 / 2.60 ( 1104) hydrogen bonds : angle 3.85606 / 2.81 ( 3276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6026.20 seconds wall clock time: 103 minutes 11.55 seconds (6191.55 seconds total)