Starting phenix.real_space_refine on Thu Feb 5 07:37:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vec_64997/02_2026/9vec_64997.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vec_64997/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9vec_64997/02_2026/9vec_64997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vec_64997/02_2026/9vec_64997.map" model { file = "/net/cci-nas-00/data/ceres_data/9vec_64997/02_2026/9vec_64997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vec_64997/02_2026/9vec_64997.cif" } 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-2.0-5952/lib/python3.9/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, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, E, H, C, F, L, A, D, G Time building chain proxies: 2.54, per 1000 atoms: 0.16 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: 1.24 Conformation dependent library (CDL) restraints added in 673.1 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: 0.39 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: 2.46 Time building geometry restraints manager: 1.57 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: 0.05 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: 0.870 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.270 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 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 covalent geometry : bond 0.01003 (16176) covalent geometry : angle 0.66081 (21932) hydrogen bonds : bond 0.13827 ( 1104) hydrogen bonds : angle 6.08396 ( 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 : 0.451 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: 0.7478 time to fit residues: 234.4672 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 : 0.587 ------------------------------------------------------------------------------- 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: 0.9990 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: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3988 r_free = 0.3988 target = 0.176283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.144398 restraints weight = 16718.528| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.91 r_work: 0.3258 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16176 Z= 0.129 Angle : 0.490 5.602 21932 Z= 0.271 Chirality : 0.039 0.160 2532 Planarity : 0.004 0.036 2780 Dihedral : 4.054 26.723 2244 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.22 % Allowed : 8.97 % 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: 0.31 (0.18), residues: 2048 helix: 0.83 (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 0.015 0.002 TYR G 125 PHE 0.013 0.001 PHE H 66 TRP 0.020 0.002 TRP A 379 HIS 0.002 0.001 HIS A 363 Details of bonding type rmsd covalent geometry : bond 0.00286 (16176) covalent geometry : angle 0.49024 (21932) hydrogen bonds : bond 0.04102 ( 1104) hydrogen bonds : angle 4.20512 ( 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 262 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 243 time to evaluate : 0.563 Fit side-chains REVERT: K 15 GLU cc_start: 0.7059 (tp30) cc_final: 0.6735 (tp30) REVERT: K 37 MET cc_start: 0.8802 (mtp) cc_final: 0.8378 (mtp) REVERT: J 112 ASN cc_start: 0.7887 (m-40) cc_final: 0.7599 (m110) REVERT: J 295 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8375 (mt-10) REVERT: B 15 GLU cc_start: 0.7124 (tp30) cc_final: 0.6820 (tp30) REVERT: B 37 MET cc_start: 0.8810 (mtp) cc_final: 0.8449 (mtp) REVERT: E 15 GLU cc_start: 0.6930 (tp30) cc_final: 0.6634 (tp30) REVERT: E 37 MET cc_start: 0.8787 (mtp) cc_final: 0.8426 (mtp) REVERT: E 38 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7670 (mtp180) REVERT: E 43 ASN cc_start: 0.8407 (t0) cc_final: 0.7824 (p0) REVERT: E 124 GLU cc_start: 0.8604 (tt0) cc_final: 0.8299 (tt0) REVERT: H 15 GLU cc_start: 0.7072 (tp30) cc_final: 0.6736 (tp30) REVERT: H 37 MET cc_start: 0.8785 (mtp) cc_final: 0.8428 (mtp) REVERT: H 38 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7773 (mtp180) REVERT: H 91 ARG cc_start: 0.8923 (mtt90) cc_final: 0.8721 (mtm-85) REVERT: A 395 TYR cc_start: 0.8355 (m-80) cc_final: 0.8084 (m-80) REVERT: A 560 GLN cc_start: 0.7846 (tp40) cc_final: 0.7256 (tp-100) REVERT: D 188 TRP cc_start: 0.6582 (m100) cc_final: 0.6313 (m-90) REVERT: D 395 TYR cc_start: 0.8364 (m-80) cc_final: 0.8117 (m-80) REVERT: D 539 ARG cc_start: 0.8412 (mtt180) cc_final: 0.8170 (mtm-85) REVERT: D 553 MET cc_start: 0.9503 (mmm) cc_final: 0.9069 (mmm) REVERT: D 555 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7542 (mmt180) REVERT: D 560 GLN cc_start: 0.7970 (tp40) cc_final: 0.7453 (tp-100) REVERT: D 562 ARG cc_start: 0.7617 (ttm-80) cc_final: 0.7372 (ttm-80) REVERT: G 106 VAL cc_start: 0.7071 (t) cc_final: 0.6801 (p) outliers start: 19 outliers final: 4 residues processed: 250 average time/residue: 0.6973 time to fit residues: 188.3389 Evaluate side-chains 224 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 217 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 106 VAL 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 D residue 172 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: 1.9990 chunk 111 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 156 optimal weight: 0.7980 chunk 138 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** G 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.172690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.139217 restraints weight = 16943.724| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.94 r_work: 0.3209 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16176 Z= 0.160 Angle : 0.521 6.488 21932 Z= 0.281 Chirality : 0.040 0.160 2532 Planarity : 0.004 0.036 2780 Dihedral : 3.946 23.555 2244 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.63 % Allowed : 10.26 % Favored : 87.12 % 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: 0.71 (0.18), residues: 2048 helix: 1.03 (0.13), residues: 1568 sheet: None (None), residues: 0 loop : -1.22 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 562 TYR 0.017 0.002 TYR G 545 PHE 0.016 0.002 PHE D 340 TRP 0.019 0.002 TRP G 379 HIS 0.002 0.001 HIS A 363 Details of bonding type rmsd covalent geometry : bond 0.00381 (16176) covalent geometry : angle 0.52057 (21932) hydrogen bonds : bond 0.04601 ( 1104) hydrogen bonds : angle 4.17278 ( 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 271 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 230 time to evaluate : 0.529 Fit side-chains REVERT: K 37 MET cc_start: 0.8823 (mtp) cc_final: 0.8471 (mtp) REVERT: K 38 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7833 (mtp180) REVERT: K 120 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8200 (mt-10) REVERT: K 144 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7440 (mp10) REVERT: J 112 ASN cc_start: 0.8048 (m-40) cc_final: 0.7749 (m110) REVERT: J 555 ARG cc_start: 0.8153 (tpt90) cc_final: 0.7852 (mmt180) REVERT: B 15 GLU cc_start: 0.7293 (tp30) cc_final: 0.7065 (tp30) REVERT: B 37 MET cc_start: 0.8787 (mtp) cc_final: 0.8423 (mtp) REVERT: B 38 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.7811 (mtp180) REVERT: B 120 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8173 (mt-10) REVERT: B 144 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7453 (mp10) REVERT: E 37 MET cc_start: 0.8790 (mtp) cc_final: 0.8454 (mtp) REVERT: E 38 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7873 (mtp180) REVERT: H 37 MET cc_start: 0.8789 (mtp) cc_final: 0.8454 (mtp) REVERT: H 38 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7786 (mtp180) REVERT: H 120 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8191 (mt-10) REVERT: H 144 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.7496 (mp10) REVERT: A 112 ASN cc_start: 0.8019 (m110) cc_final: 0.7815 (m-40) REVERT: A 560 GLN cc_start: 0.7900 (tp40) cc_final: 0.7276 (tp-100) REVERT: D 188 TRP cc_start: 0.6784 (m100) cc_final: 0.6544 (m-90) REVERT: D 539 ARG cc_start: 0.8487 (mtt180) cc_final: 0.8201 (mtm-85) REVERT: D 553 MET cc_start: 0.9365 (mmm) cc_final: 0.9063 (mmm) REVERT: D 555 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7556 (mmt180) REVERT: D 560 GLN cc_start: 0.7874 (tp40) cc_final: 0.7380 (tp-100) REVERT: D 562 ARG cc_start: 0.7657 (ttm-80) cc_final: 0.7427 (ttp-170) REVERT: G 112 ASN cc_start: 0.7730 (m-40) cc_final: 0.7498 (m110) REVERT: G 170 GLU cc_start: 0.7425 (tt0) cc_final: 0.7183 (tt0) REVERT: G 560 GLN cc_start: 0.7399 (tt0) cc_final: 0.6841 (tp-100) outliers start: 41 outliers final: 17 residues processed: 250 average time/residue: 0.6413 time to fit residues: 174.3875 Evaluate side-chains 232 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 72 MET Chi-restraints excluded: chain B residue 144 GLN 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 144 GLN 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 172 VAL 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 555 ARG Chi-restraints excluded: chain G residue 559 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 162 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 103 optimal weight: 40.0000 chunk 76 optimal weight: 0.7980 chunk 138 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 10 optimal weight: 0.0470 chunk 71 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 54 ASN J 260 GLN J 357 GLN B 54 ASN E 54 ASN H 54 ASN A 260 GLN A 357 GLN A 549 HIS D 147 GLN D 260 GLN 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 = 0.3974 r_free = 0.3974 target = 0.175094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.140460 restraints weight = 16820.359| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.96 r_work: 0.3237 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16176 Z= 0.107 Angle : 0.461 8.181 21932 Z= 0.244 Chirality : 0.037 0.156 2532 Planarity : 0.003 0.034 2780 Dihedral : 3.557 21.627 2244 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.56 % Allowed : 12.37 % Favored : 85.06 % 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 : -0.94 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 562 TYR 0.012 0.001 TYR D 545 PHE 0.014 0.001 PHE A 332 TRP 0.015 0.001 TRP G 379 HIS 0.002 0.000 HIS G 363 Details of bonding type rmsd covalent geometry : bond 0.00237 (16176) covalent geometry : angle 0.46150 (21932) hydrogen bonds : bond 0.03641 ( 1104) hydrogen bonds : angle 3.80487 ( 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 279 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 239 time to evaluate : 0.409 Fit side-chains REVERT: K 37 MET cc_start: 0.8782 (mtp) cc_final: 0.8418 (mtp) REVERT: K 38 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7799 (mtp180) REVERT: J 112 ASN cc_start: 0.7732 (m-40) cc_final: 0.7296 (m-40) REVERT: J 125 TYR cc_start: 0.6241 (t80) cc_final: 0.5981 (t80) REVERT: B 37 MET cc_start: 0.8771 (mtp) cc_final: 0.8399 (mtp) REVERT: B 38 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7775 (mtp180) REVERT: B 125 MET cc_start: 0.9053 (ttt) cc_final: 0.8748 (ttt) REVERT: E 37 MET cc_start: 0.8780 (mtp) cc_final: 0.8412 (mtp) REVERT: E 38 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7801 (mtp180) REVERT: E 124 GLU cc_start: 0.8579 (tt0) cc_final: 0.8230 (tt0) REVERT: H 37 MET cc_start: 0.8766 (mtp) cc_final: 0.8395 (mtp) REVERT: H 38 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7740 (mtp180) REVERT: H 120 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8078 (mt-10) REVERT: H 125 MET cc_start: 0.9008 (ttt) cc_final: 0.8605 (ttt) REVERT: A 125 TYR cc_start: 0.6063 (t80) cc_final: 0.5851 (t80) REVERT: A 395 TYR cc_start: 0.8227 (m-80) cc_final: 0.8014 (m-80) REVERT: A 560 GLN cc_start: 0.7898 (tp40) cc_final: 0.7257 (tp-100) REVERT: D 539 ARG cc_start: 0.8527 (mtt180) cc_final: 0.8247 (mtm-85) REVERT: D 553 MET cc_start: 0.9433 (mmm) cc_final: 0.9067 (mmm) REVERT: D 560 GLN cc_start: 0.7879 (tp40) cc_final: 0.7385 (tp-100) REVERT: D 562 ARG cc_start: 0.7631 (ttm-80) cc_final: 0.7380 (ttp-170) REVERT: G 112 ASN cc_start: 0.7833 (m-40) cc_final: 0.7514 (m110) REVERT: G 135 VAL cc_start: 0.3433 (OUTLIER) cc_final: 0.3090 (m) REVERT: G 233 LEU cc_start: 0.6979 (mt) cc_final: 0.6759 (mp) REVERT: G 560 GLN cc_start: 0.7275 (tt0) cc_final: 0.6662 (tp-100) outliers start: 40 outliers final: 12 residues processed: 267 average time/residue: 0.6423 time to fit residues: 186.4443 Evaluate side-chains 234 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 217 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 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 G residue 135 VAL 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: 1.9990 chunk 79 optimal weight: 10.0000 chunk 166 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 174 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 54 ASN J 260 GLN J 357 GLN B 54 ASN E 54 ASN H 54 ASN A 260 GLN A 357 GLN A 531 GLN D 260 GLN G 260 GLN G 357 GLN ** G 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.172046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.139217 restraints weight = 16954.875| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.78 r_work: 0.3209 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16176 Z= 0.150 Angle : 0.514 8.753 21932 Z= 0.269 Chirality : 0.039 0.225 2532 Planarity : 0.003 0.041 2780 Dihedral : 3.644 18.735 2244 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.56 % Allowed : 14.23 % Favored : 83.21 % 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: 1.49 (0.18), residues: 2048 helix: 1.59 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.81 (0.25), residues: 504 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 0.015 0.002 TRP J 379 HIS 0.002 0.001 HIS G 363 Details of bonding type rmsd covalent geometry : bond 0.00357 (16176) covalent geometry : angle 0.51365 (21932) hydrogen bonds : bond 0.04306 ( 1104) hydrogen bonds : angle 3.95348 ( 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 262 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 222 time to evaluate : 0.589 Fit side-chains REVERT: K 15 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6866 (tm-30) REVERT: K 37 MET cc_start: 0.8817 (mtp) cc_final: 0.8448 (mtp) REVERT: K 38 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7865 (mtp180) REVERT: K 120 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8137 (mt-10) REVERT: K 144 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.7391 (mp10) REVERT: J 112 ASN cc_start: 0.7902 (m-40) cc_final: 0.7571 (m110) REVERT: B 15 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6861 (tp30) REVERT: B 37 MET cc_start: 0.8802 (mtp) cc_final: 0.8420 (mtp) REVERT: B 38 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7782 (mtp180) REVERT: B 120 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8123 (mt-10) REVERT: E 37 MET cc_start: 0.8796 (mtp) cc_final: 0.8439 (mtp) REVERT: E 38 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.7810 (mtp180) REVERT: E 144 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.7412 (mp10) REVERT: H 37 MET cc_start: 0.8798 (mtp) cc_final: 0.8421 (mtp) REVERT: H 38 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7801 (mtp180) REVERT: H 144 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.7408 (mp10) REVERT: A 125 TYR cc_start: 0.6154 (t80) cc_final: 0.5943 (t80) REVERT: A 555 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7758 (mmt180) REVERT: D 539 ARG cc_start: 0.8466 (mtt180) cc_final: 0.8223 (mtm-85) REVERT: D 553 MET cc_start: 0.9362 (mmm) cc_final: 0.9097 (mmm) REVERT: D 555 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7565 (mmt180) REVERT: D 560 GLN cc_start: 0.7975 (tp40) cc_final: 0.7426 (tp-100) REVERT: D 562 ARG cc_start: 0.7649 (ttm-80) cc_final: 0.7334 (ttm-80) REVERT: G 112 ASN cc_start: 0.8004 (m-40) cc_final: 0.7734 (m110) REVERT: G 560 GLN cc_start: 0.7363 (tt0) cc_final: 0.6987 (tp-100) outliers start: 40 outliers final: 19 residues processed: 241 average time/residue: 0.6327 time to fit residues: 166.1609 Evaluate side-chains 245 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 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 233 LEU 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 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 288 VAL 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 106 VAL Chi-restraints excluded: chain G residue 135 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: 4.9990 chunk 87 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 101 optimal weight: 0.3980 chunk 121 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 G 260 GLN G 357 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.172477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.127838 restraints weight = 17753.108| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.81 r_work: 0.3225 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3308 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= 0.116 Angle : 0.472 8.116 21932 Z= 0.246 Chirality : 0.038 0.229 2532 Planarity : 0.003 0.033 2780 Dihedral : 3.467 17.432 2244 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.37 % Allowed : 15.45 % Favored : 82.18 % 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: 1.82 (0.19), residues: 2048 helix: 1.80 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.59 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 562 TYR 0.014 0.001 TYR D 545 PHE 0.011 0.001 PHE D 332 TRP 0.014 0.001 TRP G 379 HIS 0.002 0.000 HIS J 363 Details of bonding type rmsd covalent geometry : bond 0.00266 (16176) covalent geometry : angle 0.47217 (21932) hydrogen bonds : bond 0.03771 ( 1104) hydrogen bonds : angle 3.79024 ( 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 271 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 234 time to evaluate : 0.597 Fit side-chains REVERT: K 15 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6863 (tm-30) REVERT: K 37 MET cc_start: 0.8704 (mtp) cc_final: 0.8319 (mtp) REVERT: K 38 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7589 (mtp180) REVERT: K 120 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8084 (mt-10) REVERT: J 112 ASN cc_start: 0.7720 (m-40) cc_final: 0.7374 (m110) REVERT: B 37 MET cc_start: 0.8730 (mtp) cc_final: 0.8342 (mtp) REVERT: B 38 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7583 (mtp180) REVERT: B 120 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8063 (mt-10) REVERT: E 37 MET cc_start: 0.8703 (mtp) cc_final: 0.8319 (mtp) REVERT: E 38 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7619 (mtp180) REVERT: H 15 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6838 (tm-30) REVERT: H 37 MET cc_start: 0.8729 (mtp) cc_final: 0.8346 (mtp) REVERT: H 38 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7568 (mtp180) REVERT: H 120 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8066 (mt-10) REVERT: A 112 ASN cc_start: 0.7600 (m110) cc_final: 0.7395 (m-40) REVERT: A 560 GLN cc_start: 0.7968 (tp40) cc_final: 0.7280 (tp-100) REVERT: D 539 ARG cc_start: 0.8394 (mtt180) cc_final: 0.8129 (mtm-85) REVERT: D 553 MET cc_start: 0.9401 (mmm) cc_final: 0.9085 (mmm) REVERT: D 560 GLN cc_start: 0.7902 (tp40) cc_final: 0.7369 (tp-100) REVERT: D 562 ARG cc_start: 0.7541 (ttm-80) cc_final: 0.7338 (mtp85) REVERT: G 112 ASN cc_start: 0.7860 (m-40) cc_final: 0.7586 (m110) REVERT: G 560 GLN cc_start: 0.7204 (tt0) cc_final: 0.6777 (tp-100) outliers start: 37 outliers final: 14 residues processed: 256 average time/residue: 0.6501 time to fit residues: 180.9757 Evaluate side-chains 239 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 219 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 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 15 GLU Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 72 MET 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 G residue 135 VAL 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: 2.9990 chunk 120 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 170 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 44 optimal weight: 0.0270 chunk 161 optimal weight: 0.0170 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 549 HIS G 260 GLN G 357 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.171074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.123505 restraints weight = 17601.061| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.86 r_work: 0.3266 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3462 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= 0.104 Angle : 0.464 10.197 21932 Z= 0.239 Chirality : 0.037 0.247 2532 Planarity : 0.003 0.031 2780 Dihedral : 3.350 15.841 2244 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.69 % Allowed : 15.51 % Favored : 81.79 % 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: 2.06 (0.19), residues: 2048 helix: 1.97 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.49 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 562 TYR 0.012 0.001 TYR G 545 PHE 0.010 0.001 PHE G 332 TRP 0.013 0.001 TRP J 379 HIS 0.002 0.000 HIS D 509 Details of bonding type rmsd covalent geometry : bond 0.00230 (16176) covalent geometry : angle 0.46412 (21932) hydrogen bonds : bond 0.03544 ( 1104) hydrogen bonds : angle 3.71015 ( 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 273 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 231 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: K 37 MET cc_start: 0.8672 (mtp) cc_final: 0.8293 (mtp) REVERT: K 38 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7613 (mtp180) REVERT: K 120 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8039 (mt-10) REVERT: J 112 ASN cc_start: 0.7632 (m-40) cc_final: 0.7380 (m110) REVERT: J 239 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7783 (mt) REVERT: J 555 ARG cc_start: 0.7711 (mtp85) cc_final: 0.7238 (mtt-85) REVERT: B 15 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6887 (tp30) REVERT: B 37 MET cc_start: 0.8667 (mtp) cc_final: 0.8285 (mtp) REVERT: B 38 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7569 (mtp180) REVERT: B 120 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8038 (mt-10) REVERT: E 38 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7594 (mtp180) REVERT: H 15 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6807 (tm-30) REVERT: H 38 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7590 (mtp180) REVERT: H 120 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8045 (mt-10) REVERT: A 555 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7552 (mmt180) REVERT: A 560 GLN cc_start: 0.7887 (tp40) cc_final: 0.7132 (tp-100) REVERT: D 539 ARG cc_start: 0.8395 (mtt180) cc_final: 0.8116 (mtm-85) REVERT: D 553 MET cc_start: 0.9408 (mmm) cc_final: 0.9080 (mmm) REVERT: D 555 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7308 (mmt180) REVERT: D 560 GLN cc_start: 0.7906 (tp40) cc_final: 0.7380 (tp-100) REVERT: D 562 ARG cc_start: 0.7502 (ttm-80) cc_final: 0.7249 (ttp-170) REVERT: G 112 ASN cc_start: 0.7702 (m-40) cc_final: 0.7354 (m110) REVERT: G 560 GLN cc_start: 0.7200 (tt0) cc_final: 0.6563 (tp40) outliers start: 42 outliers final: 13 residues processed: 255 average time/residue: 0.6887 time to fit residues: 191.2770 Evaluate side-chains 245 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 165 VAL Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 239 LEU 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 15 GLU Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 72 MET 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 135 VAL 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: 0.0040 chunk 142 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 167 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 200 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 G 357 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.170087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.121714 restraints weight = 17785.356| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.93 r_work: 0.3224 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16176 Z= 0.117 Angle : 0.481 11.101 21932 Z= 0.249 Chirality : 0.038 0.294 2532 Planarity : 0.003 0.033 2780 Dihedral : 3.362 15.883 2244 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.56 % Allowed : 16.54 % Favored : 80.90 % 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: 2.02 (0.19), residues: 2048 helix: 1.93 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.48 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 562 TYR 0.014 0.001 TYR A 545 PHE 0.012 0.001 PHE G 332 TRP 0.012 0.001 TRP J 379 HIS 0.002 0.000 HIS D 509 Details of bonding type rmsd covalent geometry : bond 0.00268 (16176) covalent geometry : angle 0.48095 (21932) hydrogen bonds : bond 0.03721 ( 1104) hydrogen bonds : angle 3.77029 ( 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 267 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 227 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: K 15 GLU cc_start: 0.7279 (mm-30) cc_final: 0.7007 (tp30) REVERT: K 38 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7648 (mtp180) REVERT: K 120 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8076 (mt-10) REVERT: J 112 ASN cc_start: 0.7565 (m-40) cc_final: 0.7352 (m110) REVERT: J 239 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7773 (mt) REVERT: J 555 ARG cc_start: 0.7756 (mtp85) cc_final: 0.7289 (mtt-85) REVERT: B 15 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6893 (tp30) REVERT: B 37 MET cc_start: 0.8684 (mtp) cc_final: 0.8300 (mtp) REVERT: B 38 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7666 (mtp180) REVERT: B 120 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8072 (mt-10) REVERT: E 37 MET cc_start: 0.8668 (mtp) cc_final: 0.8341 (mtp) REVERT: E 38 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7611 (mtp180) REVERT: H 37 MET cc_start: 0.8661 (mtp) cc_final: 0.8350 (mtp) REVERT: H 38 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7626 (mtp180) REVERT: H 120 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8065 (mt-10) REVERT: A 555 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7610 (mmt180) REVERT: D 539 ARG cc_start: 0.8423 (mtt180) cc_final: 0.8166 (mtm-85) REVERT: D 553 MET cc_start: 0.9392 (mmm) cc_final: 0.9081 (mmm) REVERT: D 555 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7350 (mmt180) REVERT: D 560 GLN cc_start: 0.7919 (tp40) cc_final: 0.7350 (tp-100) REVERT: D 562 ARG cc_start: 0.7524 (ttm-80) cc_final: 0.7252 (ttm-80) REVERT: G 112 ASN cc_start: 0.7715 (m-40) cc_final: 0.7356 (m-40) REVERT: G 560 GLN cc_start: 0.7249 (tt0) cc_final: 0.6506 (tp-100) outliers start: 40 outliers final: 19 residues processed: 248 average time/residue: 0.7166 time to fit residues: 193.6053 Evaluate side-chains 253 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 226 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 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 239 LEU Chi-restraints excluded: chain B residue 15 GLU 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 10 ILE 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 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 135 VAL 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: 2.9990 chunk 34 optimal weight: 6.9990 chunk 180 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 100 optimal weight: 0.6980 chunk 165 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 G 357 GLN ** G 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.170371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.124687 restraints weight = 17667.050| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.81 r_work: 0.3195 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16176 Z= 0.157 Angle : 0.534 10.920 21932 Z= 0.276 Chirality : 0.041 0.325 2532 Planarity : 0.003 0.035 2780 Dihedral : 3.577 16.590 2244 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.44 % Allowed : 16.79 % Favored : 80.77 % 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: 1.69 (0.19), residues: 2048 helix: 1.67 (0.13), residues: 1552 sheet: None (None), residues: 0 loop : -0.55 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 562 TYR 0.017 0.002 TYR G 545 PHE 0.015 0.002 PHE A 275 TRP 0.012 0.002 TRP J 379 HIS 0.003 0.001 HIS J 509 Details of bonding type rmsd covalent geometry : bond 0.00377 (16176) covalent geometry : angle 0.53358 (21932) hydrogen bonds : bond 0.04325 ( 1104) hydrogen bonds : angle 3.95241 ( 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 268 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 230 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: K 37 MET cc_start: 0.8681 (mtp) cc_final: 0.8320 (mtp) REVERT: K 38 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7615 (mtp180) REVERT: J 112 ASN cc_start: 0.7512 (m-40) cc_final: 0.7239 (m-40) REVERT: B 37 MET cc_start: 0.8707 (mtp) cc_final: 0.8309 (mtp) REVERT: B 38 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7665 (mtp180) REVERT: B 120 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8019 (mt-10) REVERT: E 37 MET cc_start: 0.8527 (mtp) cc_final: 0.8208 (mtp) REVERT: E 38 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7618 (mtp180) REVERT: H 37 MET cc_start: 0.8558 (mtp) cc_final: 0.8233 (mtp) REVERT: H 38 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7577 (mtp180) REVERT: C 43 GLU cc_start: 0.7283 (mt-10) cc_final: 0.6997 (mt-10) REVERT: A 555 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7569 (mmt180) REVERT: D 539 ARG cc_start: 0.8364 (mtt180) cc_final: 0.8023 (ttm-80) REVERT: D 553 MET cc_start: 0.9295 (mmm) cc_final: 0.9034 (mmm) REVERT: D 555 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7356 (mmt180) REVERT: D 560 GLN cc_start: 0.7882 (tp40) cc_final: 0.7289 (tp-100) REVERT: D 562 ARG cc_start: 0.7575 (ttm-80) cc_final: 0.7290 (ttm-80) REVERT: G 112 ASN cc_start: 0.7593 (m-40) cc_final: 0.7323 (m-40) REVERT: G 560 GLN cc_start: 0.7285 (tt0) cc_final: 0.7075 (tt0) outliers start: 38 outliers final: 20 residues processed: 249 average time/residue: 0.7186 time to fit residues: 194.2571 Evaluate side-chains 251 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 225 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 B residue 10 ILE 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 10 ILE 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 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 135 VAL 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: 0.9990 chunk 129 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 103 optimal weight: 20.0000 chunk 89 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 195 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 196 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 G 357 GLN G 560 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.168776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.119524 restraints weight = 17749.408| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.74 r_work: 0.3213 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3578 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= 0.125 Angle : 0.506 11.968 21932 Z= 0.258 Chirality : 0.039 0.308 2532 Planarity : 0.003 0.033 2780 Dihedral : 3.464 16.535 2244 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.05 % Allowed : 17.18 % Favored : 80.77 % 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: 1.86 (0.19), residues: 2048 helix: 1.80 (0.13), residues: 1552 sheet: None (None), residues: 0 loop : -0.51 (0.26), residues: 496 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 0.014 0.001 PHE G 275 TRP 0.013 0.001 TRP J 379 HIS 0.002 0.000 HIS D 509 Details of bonding type rmsd covalent geometry : bond 0.00290 (16176) covalent geometry : angle 0.50618 (21932) hydrogen bonds : bond 0.03847 ( 1104) hydrogen bonds : angle 3.83267 ( 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 257 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: K 15 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6961 (tp30) REVERT: K 37 MET cc_start: 0.8575 (mtp) cc_final: 0.8235 (mtp) REVERT: K 38 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7547 (mtp180) REVERT: K 120 GLU cc_start: 0.8292 (mt-10) cc_final: 0.8014 (mt-10) REVERT: B 15 GLU cc_start: 0.7054 (tp30) cc_final: 0.6768 (tp30) REVERT: B 37 MET cc_start: 0.8630 (mtp) cc_final: 0.8242 (mtp) REVERT: B 38 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7503 (mtp180) REVERT: B 120 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8010 (mt-10) REVERT: E 37 MET cc_start: 0.8582 (mtp) cc_final: 0.8235 (mtp) REVERT: E 38 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7533 (mtp180) REVERT: H 37 MET cc_start: 0.8581 (mtp) cc_final: 0.8230 (mtp) REVERT: H 38 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7537 (mtp180) REVERT: A 555 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7470 (mmt180) REVERT: A 560 GLN cc_start: 0.7884 (tp40) cc_final: 0.7091 (tp-100) REVERT: D 539 ARG cc_start: 0.8345 (mtt180) cc_final: 0.8085 (mtm-85) REVERT: D 553 MET cc_start: 0.9328 (mmm) cc_final: 0.8983 (mmm) REVERT: D 555 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7195 (mmt180) REVERT: D 560 GLN cc_start: 0.7892 (tp40) cc_final: 0.7306 (tp-100) REVERT: G 112 ASN cc_start: 0.7559 (m-40) cc_final: 0.7302 (m-40) REVERT: G 560 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.6725 (tp-100) outliers start: 32 outliers final: 20 residues processed: 240 average time/residue: 0.6976 time to fit residues: 182.0087 Evaluate side-chains 246 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 219 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 B residue 10 ILE 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 10 ILE 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 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 135 VAL Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 555 ARG Chi-restraints excluded: chain G residue 560 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 56 optimal weight: 0.0970 chunk 75 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 126 optimal weight: 0.1980 chunk 143 optimal weight: 1.9990 chunk 192 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 G 357 GLN G 560 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.170108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.121627 restraints weight = 17553.803| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.73 r_work: 0.3225 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16176 Z= 0.120 Angle : 0.498 11.517 21932 Z= 0.256 Chirality : 0.039 0.306 2532 Planarity : 0.003 0.033 2780 Dihedral : 3.443 16.095 2244 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.05 % Allowed : 17.12 % Favored : 80.83 % 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: 1.92 (0.19), residues: 2048 helix: 1.84 (0.13), residues: 1552 sheet: None (None), residues: 0 loop : -0.46 (0.27), residues: 496 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 0.013 0.001 PHE D 275 TRP 0.013 0.001 TRP J 379 HIS 0.003 0.001 HIS G 509 Details of bonding type rmsd covalent geometry : bond 0.00276 (16176) covalent geometry : angle 0.49793 (21932) hydrogen bonds : bond 0.03820 ( 1104) hydrogen bonds : angle 3.82028 ( 3276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6199.46 seconds wall clock time: 105 minutes 57.16 seconds (6357.16 seconds total)