Starting phenix.real_space_refine on Thu Jul 2 22:06:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kcb_22807/07_2026/7kcb_22807.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kcb_22807/07_2026/7kcb_22807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kcb_22807/07_2026/7kcb_22807.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kcb_22807/07_2026/7kcb_22807.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7kcb_22807/07_2026/7kcb_22807.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kcb_22807/07_2026/7kcb_22807.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kcb_22807/07_2026/7kcb_22807.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kcb_22807/07_2026/7kcb_22807.map" } resolution = 2.77 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= 0.004 sd= 0.378 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: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 8 5.49 5 S 56 5.16 5 C 6648 2.51 5 N 1788 2.21 5 O 2016 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10536 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2582 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 333} Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {' ZN': 2, 'ETF': 1, 'NAD': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 340 SG CYS A 43 24.343 24.842 37.230 1.00 44.63 S ATOM 1159 SG CYS A 153 27.829 26.711 36.626 1.00 39.07 S ATOM 747 SG CYS A 97 34.965 44.773 29.715 1.00 47.83 S ATOM 766 SG CYS A 100 34.515 45.294 33.347 1.00 42.66 S ATOM 793 SG CYS A 103 35.835 42.103 32.542 1.00 40.41 S ATOM 851 SG CYS A 111 32.308 42.848 31.855 1.00 44.33 S Restraints were copied for chains: B, C, D Time building chain proxies: 2.20, per 1000 atoms: 0.21 Number of scatterers: 10536 At special positions: 0 Unit cell: (87.15, 80.85, 108.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 56 16.00 P 8 15.00 F 12 9.00 O 2016 8.00 N 1788 7.00 C 6648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS D 277 " distance=2.09 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS C 277 " distance=2.09 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 437.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS A 66 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 43 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 153 " pdb=" ZN A 402 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 111 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 97 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 100 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 103 " pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 66 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 43 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 153 " pdb=" ZN B 402 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 111 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 97 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 100 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 103 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" NE2 HIS C 66 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 43 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 153 " pdb=" ZN C 402 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 111 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 100 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 103 " pdb=" ZN D 401 " pdb="ZN ZN D 401 " - pdb=" NE2 HIS D 66 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 43 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 153 " pdb=" ZN D 402 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 111 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 97 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 100 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 103 " Number of angles added : 24 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 20 sheets defined 31.7% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 43 through 52 removed outlier: 3.800A pdb=" N LEU A 47 " --> pdb=" O CYS A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 153 through 165 Processing helix chain 'A' and resid 182 through 194 removed outlier: 3.992A pdb=" N GLN A 188 " --> pdb=" O SER A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 226 through 234 Processing helix chain 'A' and resid 248 through 256 removed outlier: 3.521A pdb=" N ILE A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 286 Processing helix chain 'A' and resid 297 through 310 Processing helix chain 'A' and resid 324 through 333 Processing helix chain 'B' and resid 43 through 52 removed outlier: 3.800A pdb=" N LEU B 47 " --> pdb=" O CYS B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 144 through 149 Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 153 through 165 Processing helix chain 'B' and resid 182 through 194 removed outlier: 3.992A pdb=" N GLN B 188 " --> pdb=" O SER B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 226 through 234 Processing helix chain 'B' and resid 248 through 256 removed outlier: 3.521A pdb=" N ILE B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR B 256 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 286 Processing helix chain 'B' and resid 297 through 310 Processing helix chain 'B' and resid 324 through 333 Processing helix chain 'C' and resid 43 through 52 removed outlier: 3.800A pdb=" N LEU C 47 " --> pdb=" O CYS C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 106 Processing helix chain 'C' and resid 144 through 149 Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 153 through 165 Processing helix chain 'C' and resid 182 through 194 removed outlier: 3.992A pdb=" N GLN C 188 " --> pdb=" O SER C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 213 Processing helix chain 'C' and resid 226 through 234 Processing helix chain 'C' and resid 248 through 256 removed outlier: 3.521A pdb=" N ILE C 252 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR C 256 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 286 Processing helix chain 'C' and resid 297 through 310 Processing helix chain 'C' and resid 324 through 333 Processing helix chain 'D' and resid 43 through 52 removed outlier: 3.800A pdb=" N LEU D 47 " --> pdb=" O CYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 144 through 149 Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 153 through 165 Processing helix chain 'D' and resid 182 through 194 removed outlier: 3.992A pdb=" N GLN D 188 " --> pdb=" O SER D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 213 Processing helix chain 'D' and resid 226 through 234 Processing helix chain 'D' and resid 248 through 256 removed outlier: 3.521A pdb=" N ILE D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR D 256 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 286 Processing helix chain 'D' and resid 297 through 310 Processing helix chain 'D' and resid 324 through 333 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 10 Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 132 removed outlier: 6.815A pdb=" N LEU A 34 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA A 69 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR A 87 " --> pdb=" O ILE A 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 132 removed outlier: 4.703A pdb=" N TYR A 341 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LYS A 318 " --> pdb=" O VAL A 342 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASP A 344 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL A 320 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 93 through 95 Processing sheet with id=AA5, first strand: chain 'A' and resid 217 through 220 removed outlier: 6.191A pdb=" N VAL A 173 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE A 200 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE A 175 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TRP A 172 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N HIS A 240 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N VAL A 266 " --> pdb=" O HIS A 240 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL A 242 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N HIS D 240 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N VAL D 266 " --> pdb=" O HIS D 240 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL D 242 " --> pdb=" O VAL D 266 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TRP D 172 " --> pdb=" O ALA D 239 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL D 173 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE D 200 " --> pdb=" O VAL D 173 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE D 175 " --> pdb=" O ILE D 200 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 275 through 279 Processing sheet with id=AA7, first strand: chain 'B' and resid 5 through 10 Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 132 removed outlier: 6.815A pdb=" N LEU B 34 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA B 69 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR B 87 " --> pdb=" O ILE B 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 132 removed outlier: 4.703A pdb=" N TYR B 341 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LYS B 318 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASP B 344 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL B 320 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 93 through 95 Processing sheet with id=AB2, first strand: chain 'B' and resid 217 through 220 removed outlier: 6.191A pdb=" N VAL B 173 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE B 200 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE B 175 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TRP B 172 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N HIS B 240 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N VAL B 266 " --> pdb=" O HIS B 240 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL B 242 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N HIS C 240 " --> pdb=" O THR C 264 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N VAL C 266 " --> pdb=" O HIS C 240 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL C 242 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TRP C 172 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL C 173 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE C 200 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE C 175 " --> pdb=" O ILE C 200 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 275 through 279 Processing sheet with id=AB4, first strand: chain 'C' and resid 5 through 10 Processing sheet with id=AB5, first strand: chain 'C' and resid 128 through 132 removed outlier: 6.815A pdb=" N LEU C 34 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA C 69 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR C 87 " --> pdb=" O ILE C 139 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 128 through 132 removed outlier: 4.703A pdb=" N TYR C 341 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LYS C 318 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASP C 344 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL C 320 " --> pdb=" O ASP C 344 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 93 through 95 Processing sheet with id=AB8, first strand: chain 'D' and resid 5 through 10 Processing sheet with id=AB9, first strand: chain 'D' and resid 128 through 132 removed outlier: 6.815A pdb=" N LEU D 34 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA D 69 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR D 87 " --> pdb=" O ILE D 139 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 128 through 132 removed outlier: 4.703A pdb=" N TYR D 341 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LYS D 318 " --> pdb=" O VAL D 342 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASP D 344 " --> pdb=" O LYS D 318 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL D 320 " --> pdb=" O ASP D 344 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 93 through 95 416 hydrogen bonds defined for protein. 1176 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: 2.08 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3416 1.34 - 1.46: 2540 1.46 - 1.59: 4704 1.59 - 1.71: 16 1.71 - 1.84: 80 Bond restraints: 10756 Sorted by residual: bond pdb=" CB VAL C 58 " pdb=" CG1 VAL C 58 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.22e+00 bond pdb=" CB VAL D 58 " pdb=" CG1 VAL D 58 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.22e+00 bond pdb=" CB VAL A 58 " pdb=" CG1 VAL A 58 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.22e+00 bond pdb=" CB VAL B 58 " pdb=" CG1 VAL B 58 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.22e+00 bond pdb=" O3 NAD D 403 " pdb=" PA NAD D 403 " ideal model delta sigma weight residual 1.653 1.600 0.053 2.00e-02 2.50e+03 7.06e+00 ... (remaining 10751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 13576 1.65 - 3.30: 868 3.30 - 4.94: 140 4.94 - 6.59: 20 6.59 - 8.24: 8 Bond angle restraints: 14612 Sorted by residual: angle pdb=" C ALA B 234 " pdb=" N THR B 235 " pdb=" CA THR B 235 " ideal model delta sigma weight residual 122.11 128.85 -6.74 1.64e+00 3.72e-01 1.69e+01 angle pdb=" C ALA D 234 " pdb=" N THR D 235 " pdb=" CA THR D 235 " ideal model delta sigma weight residual 122.11 128.85 -6.74 1.64e+00 3.72e-01 1.69e+01 angle pdb=" C ALA C 234 " pdb=" N THR C 235 " pdb=" CA THR C 235 " ideal model delta sigma weight residual 122.11 128.85 -6.74 1.64e+00 3.72e-01 1.69e+01 angle pdb=" C ALA A 234 " pdb=" N THR A 235 " pdb=" CA THR A 235 " ideal model delta sigma weight residual 122.11 128.85 -6.74 1.64e+00 3.72e-01 1.69e+01 angle pdb=" N THR A 235 " pdb=" CA THR A 235 " pdb=" CB THR A 235 " ideal model delta sigma weight residual 110.67 105.61 5.06 1.39e+00 5.18e-01 1.33e+01 ... (remaining 14607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 5338 16.66 - 33.33: 604 33.33 - 49.99: 196 49.99 - 66.65: 56 66.65 - 83.31: 12 Dihedral angle restraints: 6206 sinusoidal: 2342 harmonic: 3864 Sorted by residual: dihedral pdb=" CA SER B 1 " pdb=" C SER B 1 " pdb=" N ILE B 2 " pdb=" CA ILE B 2 " ideal model delta harmonic sigma weight residual 180.00 159.90 20.10 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA SER D 1 " pdb=" C SER D 1 " pdb=" N ILE D 2 " pdb=" CA ILE D 2 " ideal model delta harmonic sigma weight residual 180.00 159.90 20.10 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA SER C 1 " pdb=" C SER C 1 " pdb=" N ILE C 2 " pdb=" CA ILE C 2 " ideal model delta harmonic sigma weight residual 180.00 159.90 20.10 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 6203 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.066: 1148 0.066 - 0.130: 408 0.130 - 0.195: 56 0.195 - 0.260: 8 0.260 - 0.325: 4 Chirality restraints: 1624 Sorted by residual: chirality pdb=" CB VAL D 58 " pdb=" CA VAL D 58 " pdb=" CG1 VAL D 58 " pdb=" CG2 VAL D 58 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CB VAL B 58 " pdb=" CA VAL B 58 " pdb=" CG1 VAL B 58 " pdb=" CG2 VAL B 58 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CB VAL A 58 " pdb=" CA VAL A 58 " pdb=" CG1 VAL A 58 " pdb=" CG2 VAL A 58 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 1621 not shown) Planarity restraints: 1856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 118 " 0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C GLY B 118 " -0.057 2.00e-02 2.50e+03 pdb=" O GLY B 118 " 0.021 2.00e-02 2.50e+03 pdb=" N TYR B 119 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 118 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C GLY C 118 " 0.057 2.00e-02 2.50e+03 pdb=" O GLY C 118 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR C 119 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 118 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C GLY D 118 " 0.057 2.00e-02 2.50e+03 pdb=" O GLY D 118 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR D 119 " -0.020 2.00e-02 2.50e+03 ... (remaining 1853 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2602 2.79 - 3.31: 9622 3.31 - 3.84: 19314 3.84 - 4.37: 24644 4.37 - 4.90: 40614 Nonbonded interactions: 96796 Sorted by model distance: nonbonded pdb="ZN ZN A 401 " pdb=" O ETF A 404 " model vdw 2.258 2.230 nonbonded pdb="ZN ZN C 401 " pdb=" O ETF C 404 " model vdw 2.258 2.230 nonbonded pdb="ZN ZN D 401 " pdb=" O ETF D 404 " model vdw 2.258 2.230 nonbonded pdb="ZN ZN B 401 " pdb=" O ETF B 404 " model vdw 2.258 2.230 nonbonded pdb=" O CYS C 153 " pdb=" OG1 THR C 157 " model vdw 2.324 3.040 ... (remaining 96791 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 12.910 Find NCS groups from input model: 0.110 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:8.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 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 : 0.013 0.284 10786 Z= 0.520 Angle : 0.955 10.117 14640 Z= 0.512 Chirality : 0.064 0.325 1624 Planarity : 0.006 0.063 1856 Dihedral : 16.726 83.309 3776 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.99 % Allowed : 21.64 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -3.27 (0.19), residues: 1380 helix: -2.26 (0.19), residues: 452 sheet: -1.92 (0.27), residues: 280 loop : -2.10 (0.21), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 260 TYR 0.017 0.003 TYR C 258 PHE 0.017 0.003 PHE B 221 TRP 0.010 0.002 TRP B 172 HIS 0.009 0.002 HIS B 240 Details of bonding type rmsd/Z covalent geometry : bond 0.01117 / 0.47 (10756) covalent geometry : angle 0.90995 / 0.51 (14612) SS BOND : bond 0.06347 / 3.19 ( 2) SS BOND : angle 1.70741 / 0.85 ( 4) hydrogen bonds : bond 0.16409 / 11.50 ( 400) hydrogen bonds : angle 8.51356 / 5.88 ( 1176) metal coordination : bond 0.12421 / 9.64 ( 28) metal coordination : angle 7.20305 / 4.56 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.378 Fit side-chains REVERT: A 5 THR cc_start: 0.8573 (m) cc_final: 0.8279 (t) REVERT: A 17 LYS cc_start: 0.6700 (tttm) cc_final: 0.6265 (ttpt) REVERT: A 196 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8353 (mtp180) REVERT: A 275 LYS cc_start: 0.7970 (mtmm) cc_final: 0.7762 (mttp) REVERT: B 5 THR cc_start: 0.8578 (m) cc_final: 0.8285 (t) REVERT: B 17 LYS cc_start: 0.6711 (tttm) cc_final: 0.6271 (ttpt) REVERT: B 196 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8366 (mtp180) REVERT: B 275 LYS cc_start: 0.7967 (mtmm) cc_final: 0.7759 (mttp) REVERT: C 5 THR cc_start: 0.8574 (m) cc_final: 0.8282 (t) REVERT: C 17 LYS cc_start: 0.6696 (tttm) cc_final: 0.6262 (ttpt) REVERT: C 196 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8361 (mtp180) REVERT: C 275 LYS cc_start: 0.7968 (mtmm) cc_final: 0.7762 (mttp) REVERT: D 5 THR cc_start: 0.8574 (m) cc_final: 0.8282 (t) REVERT: D 17 LYS cc_start: 0.6711 (tttm) cc_final: 0.6276 (ttpt) REVERT: D 196 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8360 (mtp180) REVERT: D 275 LYS cc_start: 0.7967 (mtmm) cc_final: 0.7760 (mttp) outliers start: 32 outliers final: 16 residues processed: 176 average time/residue: 0.5700 time to fit residues: 108.0373 Evaluate side-chains 143 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 196 ARG Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 323 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN A 135 GLN A 147 GLN B 36 ASN B 135 GLN B 147 GLN C 36 ASN C 135 GLN C 147 GLN D 36 ASN D 135 GLN D 147 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.132281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.106657 restraints weight = 9685.216| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.34 r_work: 0.2981 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 10786 Z= 0.122 Angle : 0.501 4.867 14640 Z= 0.256 Chirality : 0.045 0.137 1624 Planarity : 0.004 0.046 1856 Dihedral : 6.627 48.188 1536 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.24 % Allowed : 20.90 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.80 (0.20), residues: 1380 helix: -0.52 (0.24), residues: 452 sheet: -1.44 (0.29), residues: 240 loop : -1.51 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 310 TYR 0.015 0.001 TYR B 258 PHE 0.011 0.002 PHE B 221 TRP 0.003 0.001 TRP C 82 HIS 0.003 0.001 HIS D 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (10756) covalent geometry : angle 0.49500 / 0.26 (14612) SS BOND : bond 0.00380 / 0.19 ( 2) SS BOND : angle 0.58329 / 0.29 ( 4) hydrogen bonds : bond 0.03421 / 2.40 ( 400) hydrogen bonds : angle 5.61384 / 3.91 ( 1176) metal coordination : bond 0.00276 / 0.20 ( 28) metal coordination : angle 2.01998 / 1.39 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.7988 (t) REVERT: A 17 LYS cc_start: 0.6489 (tttm) cc_final: 0.5839 (ttpt) REVERT: A 208 GLU cc_start: 0.7011 (mp0) cc_final: 0.6757 (mp0) REVERT: A 275 LYS cc_start: 0.7900 (mtmm) cc_final: 0.7413 (mttp) REVERT: A 300 ASP cc_start: 0.8085 (m-30) cc_final: 0.7802 (m-30) REVERT: B 5 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.8000 (t) REVERT: B 17 LYS cc_start: 0.6492 (tttm) cc_final: 0.5845 (ttpt) REVERT: B 208 GLU cc_start: 0.7006 (mp0) cc_final: 0.6752 (mp0) REVERT: B 275 LYS cc_start: 0.7902 (mtmm) cc_final: 0.7419 (mttp) REVERT: B 300 ASP cc_start: 0.8064 (m-30) cc_final: 0.7776 (m-30) REVERT: C 5 THR cc_start: 0.8340 (OUTLIER) cc_final: 0.8001 (t) REVERT: C 17 LYS cc_start: 0.6500 (tttm) cc_final: 0.5843 (ttpt) REVERT: C 208 GLU cc_start: 0.7015 (mp0) cc_final: 0.6763 (mp0) REVERT: C 275 LYS cc_start: 0.7902 (mtmm) cc_final: 0.7421 (mttp) REVERT: C 300 ASP cc_start: 0.8065 (m-30) cc_final: 0.7776 (m-30) REVERT: D 5 THR cc_start: 0.8333 (OUTLIER) cc_final: 0.7994 (t) REVERT: D 17 LYS cc_start: 0.6512 (tttm) cc_final: 0.5868 (ttpt) REVERT: D 208 GLU cc_start: 0.7025 (mp0) cc_final: 0.6768 (mp0) REVERT: D 275 LYS cc_start: 0.7908 (mtmm) cc_final: 0.7426 (mttp) REVERT: D 300 ASP cc_start: 0.8141 (m-30) cc_final: 0.7866 (m-30) outliers start: 24 outliers final: 8 residues processed: 152 average time/residue: 0.5783 time to fit residues: 94.6546 Evaluate side-chains 129 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 294 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 8.9990 chunk 129 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 HIS A 147 GLN B 138 HIS B 147 GLN C 138 HIS C 147 GLN D 138 HIS D 147 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.123636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.097736 restraints weight = 9912.935| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.34 r_work: 0.2885 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 10786 Z= 0.308 Angle : 0.629 6.887 14640 Z= 0.313 Chirality : 0.050 0.138 1624 Planarity : 0.005 0.039 1856 Dihedral : 6.698 44.104 1508 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.48 % Allowed : 21.27 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.58 (0.21), residues: 1380 helix: -0.54 (0.23), residues: 456 sheet: -1.03 (0.32), residues: 236 loop : -1.34 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 310 TYR 0.019 0.002 TYR D 258 PHE 0.013 0.002 PHE B 221 TRP 0.011 0.002 TRP C 92 HIS 0.003 0.001 HIS B 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00736 / 0.31 (10756) covalent geometry : angle 0.61781 / 0.31 (14612) SS BOND : bond 0.00024 / 0.01 ( 2) SS BOND : angle 1.40294 / 0.72 ( 4) hydrogen bonds : bond 0.04090 / 2.84 ( 400) hydrogen bonds : angle 5.64440 / 3.93 ( 1176) metal coordination : bond 0.00852 / 0.59 ( 28) metal coordination : angle 2.87887 / 2.05 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 140 time to evaluate : 0.362 Fit side-chains REVERT: A 5 THR cc_start: 0.8326 (OUTLIER) cc_final: 0.8038 (t) REVERT: A 17 LYS cc_start: 0.7140 (tttm) cc_final: 0.6444 (ttpt) REVERT: A 182 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8297 (mp) REVERT: A 208 GLU cc_start: 0.7036 (mp0) cc_final: 0.6754 (mp0) REVERT: A 275 LYS cc_start: 0.8027 (mtmm) cc_final: 0.7519 (mttp) REVERT: B 5 THR cc_start: 0.8332 (OUTLIER) cc_final: 0.8040 (t) REVERT: B 17 LYS cc_start: 0.7148 (tttm) cc_final: 0.6446 (ttpt) REVERT: B 182 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8292 (mp) REVERT: B 208 GLU cc_start: 0.7066 (mp0) cc_final: 0.6784 (mp0) REVERT: B 275 LYS cc_start: 0.8013 (mtmm) cc_final: 0.7507 (mttp) REVERT: C 5 THR cc_start: 0.8332 (OUTLIER) cc_final: 0.8045 (t) REVERT: C 17 LYS cc_start: 0.7143 (tttm) cc_final: 0.6443 (ttpt) REVERT: C 182 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8296 (mp) REVERT: C 208 GLU cc_start: 0.7075 (mp0) cc_final: 0.6797 (mp0) REVERT: C 275 LYS cc_start: 0.8007 (mtmm) cc_final: 0.7472 (mttp) REVERT: C 277 CYS cc_start: 0.7902 (m) cc_final: 0.7668 (m) REVERT: D 5 THR cc_start: 0.8323 (OUTLIER) cc_final: 0.8033 (t) REVERT: D 17 LYS cc_start: 0.7151 (tttm) cc_final: 0.6453 (ttpt) REVERT: D 182 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8297 (mp) REVERT: D 208 GLU cc_start: 0.7075 (mp0) cc_final: 0.6792 (mp0) REVERT: D 275 LYS cc_start: 0.8000 (mtmm) cc_final: 0.7474 (mttp) REVERT: D 277 CYS cc_start: 0.7913 (m) cc_final: 0.7684 (m) REVERT: D 300 ASP cc_start: 0.8224 (m-30) cc_final: 0.7974 (m-30) outliers start: 48 outliers final: 32 residues processed: 184 average time/residue: 0.5054 time to fit residues: 101.3236 Evaluate side-chains 171 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 131 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 1 SER Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 1 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 313 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 15 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN B 147 GLN C 147 GLN D 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.131452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.105923 restraints weight = 9815.581| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.35 r_work: 0.2972 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10786 Z= 0.114 Angle : 0.474 5.128 14640 Z= 0.240 Chirality : 0.044 0.136 1624 Planarity : 0.004 0.033 1856 Dihedral : 6.132 39.748 1508 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.36 % Allowed : 22.20 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.12 (0.21), residues: 1380 helix: 0.09 (0.25), residues: 456 sheet: -1.21 (0.32), residues: 240 loop : -1.06 (0.21), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 260 TYR 0.015 0.001 TYR A 258 PHE 0.010 0.001 PHE C 221 TRP 0.005 0.001 TRP C 54 HIS 0.001 0.000 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (10756) covalent geometry : angle 0.46843 / 0.24 (14612) SS BOND : bond 0.00072 / 0.04 ( 2) SS BOND : angle 0.62034 / 0.32 ( 4) hydrogen bonds : bond 0.03114 / 2.20 ( 400) hydrogen bonds : angle 5.05292 / 3.55 ( 1176) metal coordination : bond 0.00181 / 0.12 ( 28) metal coordination : angle 1.78974 / 1.26 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.402 Fit side-chains REVERT: A 5 THR cc_start: 0.8242 (OUTLIER) cc_final: 0.7978 (t) REVERT: A 17 LYS cc_start: 0.6918 (tttm) cc_final: 0.6221 (ttpt) REVERT: A 77 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7411 (mt-10) REVERT: A 208 GLU cc_start: 0.6989 (mp0) cc_final: 0.6710 (mp0) REVERT: A 275 LYS cc_start: 0.7956 (mtmm) cc_final: 0.7503 (mttp) REVERT: A 347 LYS cc_start: 0.6502 (mttp) cc_final: 0.5662 (mtmt) REVERT: B 5 THR cc_start: 0.8251 (OUTLIER) cc_final: 0.7986 (t) REVERT: B 17 LYS cc_start: 0.6937 (tttm) cc_final: 0.6231 (ttpt) REVERT: B 77 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7386 (mt-10) REVERT: B 208 GLU cc_start: 0.7011 (mp0) cc_final: 0.6736 (mp0) REVERT: B 275 LYS cc_start: 0.7938 (mtmm) cc_final: 0.7496 (mttp) REVERT: B 347 LYS cc_start: 0.6495 (mttp) cc_final: 0.5671 (mtmt) REVERT: C 5 THR cc_start: 0.8268 (OUTLIER) cc_final: 0.8005 (t) REVERT: C 17 LYS cc_start: 0.6930 (tttm) cc_final: 0.6227 (ttpt) REVERT: C 77 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7348 (mt-10) REVERT: C 208 GLU cc_start: 0.7008 (mp0) cc_final: 0.6729 (mp0) REVERT: C 275 LYS cc_start: 0.7949 (mtmm) cc_final: 0.7492 (mttp) REVERT: C 277 CYS cc_start: 0.7805 (m) cc_final: 0.7573 (m) REVERT: C 300 ASP cc_start: 0.8036 (m-30) cc_final: 0.7824 (m-30) REVERT: C 347 LYS cc_start: 0.6496 (mttp) cc_final: 0.5847 (mtmt) REVERT: D 5 THR cc_start: 0.8265 (OUTLIER) cc_final: 0.8003 (t) REVERT: D 17 LYS cc_start: 0.6934 (tttm) cc_final: 0.6230 (ttpt) REVERT: D 77 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7361 (mt-10) REVERT: D 208 GLU cc_start: 0.7021 (mp0) cc_final: 0.6740 (mp0) REVERT: D 253 GLU cc_start: 0.7825 (tm-30) cc_final: 0.6682 (mt-10) REVERT: D 275 LYS cc_start: 0.7956 (mtmm) cc_final: 0.7429 (mttp) REVERT: D 277 CYS cc_start: 0.7800 (m) cc_final: 0.7579 (m) REVERT: D 300 ASP cc_start: 0.8101 (m-30) cc_final: 0.7865 (m-30) REVERT: D 347 LYS cc_start: 0.6458 (mttp) cc_final: 0.5632 (mtmt) outliers start: 36 outliers final: 12 residues processed: 166 average time/residue: 0.5315 time to fit residues: 95.8339 Evaluate side-chains 150 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 294 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 37 optimal weight: 6.9990 chunk 10 optimal weight: 0.3980 chunk 65 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 104 optimal weight: 0.0170 chunk 42 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 overall best weight: 2.2824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN B 147 GLN C 147 GLN D 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.126079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.100378 restraints weight = 9761.119| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.32 r_work: 0.2904 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10786 Z= 0.205 Angle : 0.530 5.276 14640 Z= 0.266 Chirality : 0.046 0.138 1624 Planarity : 0.004 0.030 1856 Dihedral : 6.191 38.327 1508 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.73 % Allowed : 23.13 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.18 (0.21), residues: 1380 helix: 0.00 (0.24), residues: 456 sheet: -1.21 (0.31), residues: 260 loop : -1.08 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 340 TYR 0.016 0.001 TYR D 258 PHE 0.013 0.002 PHE C 221 TRP 0.008 0.001 TRP C 92 HIS 0.002 0.001 HIS B 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (10756) covalent geometry : angle 0.52367 / 0.27 (14612) SS BOND : bond 0.00177 / 0.09 ( 2) SS BOND : angle 0.63569 / 0.33 ( 4) hydrogen bonds : bond 0.03517 / 2.46 ( 400) hydrogen bonds : angle 5.17818 / 3.64 ( 1176) metal coordination : bond 0.00524 / 0.36 ( 28) metal coordination : angle 2.13411 / 1.48 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.403 Fit side-chains REVERT: A 17 LYS cc_start: 0.7231 (tttm) cc_final: 0.6542 (ttpt) REVERT: A 182 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8457 (mp) REVERT: A 208 GLU cc_start: 0.6863 (mp0) cc_final: 0.6483 (mp0) REVERT: A 253 GLU cc_start: 0.7866 (tm-30) cc_final: 0.6772 (mt-10) REVERT: A 275 LYS cc_start: 0.8024 (mtmm) cc_final: 0.7449 (mttp) REVERT: A 347 LYS cc_start: 0.6647 (mttp) cc_final: 0.5895 (mtmt) REVERT: B 17 LYS cc_start: 0.7234 (tttm) cc_final: 0.6536 (ttpt) REVERT: B 182 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8452 (mp) REVERT: B 208 GLU cc_start: 0.6901 (mp0) cc_final: 0.6524 (mp0) REVERT: B 253 GLU cc_start: 0.7845 (tm-30) cc_final: 0.6735 (mt-10) REVERT: B 275 LYS cc_start: 0.8010 (mtmm) cc_final: 0.7433 (mttp) REVERT: B 347 LYS cc_start: 0.6648 (mttp) cc_final: 0.5889 (mtmt) REVERT: C 17 LYS cc_start: 0.7225 (tttm) cc_final: 0.6533 (ttpt) REVERT: C 182 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8445 (mp) REVERT: C 208 GLU cc_start: 0.6903 (mp0) cc_final: 0.6523 (mp0) REVERT: C 275 LYS cc_start: 0.8005 (mtmm) cc_final: 0.7500 (mttp) REVERT: C 347 LYS cc_start: 0.6645 (mttp) cc_final: 0.5892 (mtmt) REVERT: D 17 LYS cc_start: 0.7232 (tttm) cc_final: 0.6497 (ttpt) REVERT: D 182 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8452 (mp) REVERT: D 208 GLU cc_start: 0.6895 (mp0) cc_final: 0.6510 (mp0) REVERT: D 253 GLU cc_start: 0.7842 (tm-30) cc_final: 0.6745 (mt-10) REVERT: D 275 LYS cc_start: 0.8028 (mtmm) cc_final: 0.7459 (mttp) REVERT: D 300 ASP cc_start: 0.8128 (m-30) cc_final: 0.7870 (m-30) REVERT: D 347 LYS cc_start: 0.6638 (mttp) cc_final: 0.5885 (mtmt) outliers start: 40 outliers final: 23 residues processed: 173 average time/residue: 0.5435 time to fit residues: 101.7820 Evaluate side-chains 159 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 337 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 69 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 47 optimal weight: 8.9990 chunk 104 optimal weight: 0.1980 chunk 111 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN B 147 GLN C 147 GLN D 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.130358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.104646 restraints weight = 9776.122| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.35 r_work: 0.2969 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10786 Z= 0.115 Angle : 0.468 4.992 14640 Z= 0.235 Chirality : 0.044 0.135 1624 Planarity : 0.003 0.029 1856 Dihedral : 5.844 38.576 1508 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.87 % Allowed : 25.19 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.84 (0.22), residues: 1380 helix: 0.33 (0.25), residues: 456 sheet: -1.23 (0.32), residues: 240 loop : -0.83 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 260 TYR 0.014 0.001 TYR D 258 PHE 0.011 0.001 PHE A 221 TRP 0.004 0.001 TRP B 54 HIS 0.001 0.000 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (10756) covalent geometry : angle 0.46302 / 0.24 (14612) SS BOND : bond 0.00115 / 0.06 ( 2) SS BOND : angle 0.42012 / 0.21 ( 4) hydrogen bonds : bond 0.02993 / 2.12 ( 400) hydrogen bonds : angle 4.89918 / 3.45 ( 1176) metal coordination : bond 0.00152 / 0.10 ( 28) metal coordination : angle 1.76382 / 1.20 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.443 Fit side-chains REVERT: A 17 LYS cc_start: 0.7220 (tttm) cc_final: 0.6482 (ttpt) REVERT: A 208 GLU cc_start: 0.6787 (mp0) cc_final: 0.6549 (mp0) REVERT: A 253 GLU cc_start: 0.7766 (tm-30) cc_final: 0.6603 (mt-10) REVERT: A 275 LYS cc_start: 0.7897 (mtmm) cc_final: 0.7327 (mttp) REVERT: A 347 LYS cc_start: 0.6698 (mttp) cc_final: 0.5778 (mtmt) REVERT: B 17 LYS cc_start: 0.7161 (tttm) cc_final: 0.6485 (ttpt) REVERT: B 208 GLU cc_start: 0.6812 (mp0) cc_final: 0.6572 (mp0) REVERT: B 253 GLU cc_start: 0.7756 (tm-30) cc_final: 0.6607 (mt-10) REVERT: B 275 LYS cc_start: 0.7902 (mtmm) cc_final: 0.7327 (mttp) REVERT: B 347 LYS cc_start: 0.6642 (mttp) cc_final: 0.5795 (mtmt) REVERT: C 17 LYS cc_start: 0.7143 (tttm) cc_final: 0.6473 (ttpt) REVERT: C 208 GLU cc_start: 0.6843 (mp0) cc_final: 0.6603 (mp0) REVERT: C 253 GLU cc_start: 0.7751 (tm-30) cc_final: 0.6598 (mt-10) REVERT: C 275 LYS cc_start: 0.7882 (mtmm) cc_final: 0.7326 (mttp) REVERT: C 347 LYS cc_start: 0.6645 (mttp) cc_final: 0.5800 (mtmt) REVERT: D 17 LYS cc_start: 0.7150 (tttm) cc_final: 0.6484 (ttpt) REVERT: D 208 GLU cc_start: 0.6811 (mp0) cc_final: 0.6566 (mp0) REVERT: D 253 GLU cc_start: 0.7753 (tm-30) cc_final: 0.6603 (mt-10) REVERT: D 275 LYS cc_start: 0.7892 (mtmm) cc_final: 0.7346 (mttp) REVERT: D 300 ASP cc_start: 0.8071 (m-30) cc_final: 0.7844 (m-30) REVERT: D 347 LYS cc_start: 0.6672 (mttp) cc_final: 0.5761 (mtmt) outliers start: 20 outliers final: 12 residues processed: 150 average time/residue: 0.5550 time to fit residues: 90.1743 Evaluate side-chains 135 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 294 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 116 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN B 147 GLN C 121 HIS C 147 GLN D 147 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.127426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.101723 restraints weight = 9758.633| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.34 r_work: 0.2902 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10786 Z= 0.224 Angle : 0.545 5.463 14640 Z= 0.272 Chirality : 0.047 0.141 1624 Planarity : 0.004 0.028 1856 Dihedral : 6.094 38.270 1508 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.36 % Allowed : 23.13 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.22), residues: 1380 helix: 0.07 (0.24), residues: 460 sheet: -1.24 (0.31), residues: 260 loop : -0.93 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 340 TYR 0.017 0.001 TYR A 258 PHE 0.014 0.002 PHE B 221 TRP 0.008 0.001 TRP A 92 HIS 0.002 0.000 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.22 (10756) covalent geometry : angle 0.53615 / 0.27 (14612) SS BOND : bond 0.00203 / 0.10 ( 2) SS BOND : angle 0.56766 / 0.29 ( 4) hydrogen bonds : bond 0.03503 / 2.45 ( 400) hydrogen bonds : angle 5.11680 / 3.60 ( 1176) metal coordination : bond 0.00601 / 0.41 ( 28) metal coordination : angle 2.43280 / 1.62 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 0.430 Fit side-chains REVERT: A 17 LYS cc_start: 0.7283 (tttm) cc_final: 0.6589 (ttpt) REVERT: A 208 GLU cc_start: 0.6857 (mp0) cc_final: 0.6524 (mp0) REVERT: A 212 SER cc_start: 0.7561 (OUTLIER) cc_final: 0.7354 (p) REVERT: A 253 GLU cc_start: 0.7882 (tm-30) cc_final: 0.6776 (mt-10) REVERT: A 275 LYS cc_start: 0.7904 (mtmm) cc_final: 0.7329 (mttp) REVERT: A 347 LYS cc_start: 0.6681 (mttp) cc_final: 0.5691 (mtmt) REVERT: B 17 LYS cc_start: 0.7286 (tttm) cc_final: 0.6583 (ttpt) REVERT: B 208 GLU cc_start: 0.6878 (mp0) cc_final: 0.6548 (mp0) REVERT: B 212 SER cc_start: 0.7605 (OUTLIER) cc_final: 0.7400 (p) REVERT: B 253 GLU cc_start: 0.7844 (tm-30) cc_final: 0.6770 (mt-10) REVERT: B 275 LYS cc_start: 0.7893 (mtmm) cc_final: 0.7319 (mttp) REVERT: B 347 LYS cc_start: 0.6727 (mttp) cc_final: 0.5726 (mtmt) REVERT: C 17 LYS cc_start: 0.7266 (tttm) cc_final: 0.6573 (ttpt) REVERT: C 208 GLU cc_start: 0.6886 (mp0) cc_final: 0.6556 (mp0) REVERT: C 212 SER cc_start: 0.7588 (OUTLIER) cc_final: 0.7383 (p) REVERT: C 253 GLU cc_start: 0.7861 (tm-30) cc_final: 0.6777 (mt-10) REVERT: C 275 LYS cc_start: 0.7902 (mtmm) cc_final: 0.7309 (mttp) REVERT: C 347 LYS cc_start: 0.6670 (mttp) cc_final: 0.5732 (mtmt) REVERT: D 17 LYS cc_start: 0.7275 (tttm) cc_final: 0.6594 (ttpt) REVERT: D 208 GLU cc_start: 0.6881 (mp0) cc_final: 0.6542 (mp0) REVERT: D 212 SER cc_start: 0.7584 (OUTLIER) cc_final: 0.7380 (p) REVERT: D 253 GLU cc_start: 0.7839 (tm-30) cc_final: 0.6773 (mt-10) REVERT: D 275 LYS cc_start: 0.7930 (mtmm) cc_final: 0.7338 (mttp) REVERT: D 300 ASP cc_start: 0.8110 (m-30) cc_final: 0.7847 (m-30) REVERT: D 347 LYS cc_start: 0.6730 (mttp) cc_final: 0.5729 (mtmt) outliers start: 36 outliers final: 25 residues processed: 172 average time/residue: 0.5253 time to fit residues: 98.1034 Evaluate side-chains 165 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 313 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 34 optimal weight: 10.0000 chunk 83 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 98 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 42 optimal weight: 0.0060 overall best weight: 1.2798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 HIS A 147 GLN B 121 HIS B 147 GLN C 147 GLN D 121 HIS D 147 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.128798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.103121 restraints weight = 9682.116| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.33 r_work: 0.2949 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10786 Z= 0.137 Angle : 0.493 7.099 14640 Z= 0.244 Chirality : 0.045 0.137 1624 Planarity : 0.003 0.030 1856 Dihedral : 5.870 38.580 1508 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.36 % Allowed : 23.88 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.85 (0.22), residues: 1380 helix: 0.36 (0.25), residues: 460 sheet: -1.36 (0.31), residues: 264 loop : -0.77 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 260 TYR 0.015 0.001 TYR B 258 PHE 0.012 0.001 PHE B 221 TRP 0.004 0.001 TRP A 54 HIS 0.001 0.000 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (10756) covalent geometry : angle 0.48684 / 0.24 (14612) SS BOND : bond 0.00144 / 0.07 ( 2) SS BOND : angle 0.44241 / 0.23 ( 4) hydrogen bonds : bond 0.03060 / 2.16 ( 400) hydrogen bonds : angle 4.91951 / 3.47 ( 1176) metal coordination : bond 0.00239 / 0.16 ( 28) metal coordination : angle 1.91839 / 1.27 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.348 Fit side-chains REVERT: A 17 LYS cc_start: 0.7280 (tttm) cc_final: 0.6606 (ttpt) REVERT: A 208 GLU cc_start: 0.7036 (mp0) cc_final: 0.6759 (mp0) REVERT: A 253 GLU cc_start: 0.7776 (tm-30) cc_final: 0.6598 (mt-10) REVERT: A 275 LYS cc_start: 0.7822 (mtmm) cc_final: 0.7290 (mttp) REVERT: A 347 LYS cc_start: 0.6636 (mttp) cc_final: 0.5650 (mtmt) REVERT: B 17 LYS cc_start: 0.7287 (tttm) cc_final: 0.6603 (ttpt) REVERT: B 208 GLU cc_start: 0.7061 (mp0) cc_final: 0.6785 (mp0) REVERT: B 253 GLU cc_start: 0.7767 (tm-30) cc_final: 0.6589 (mt-10) REVERT: B 275 LYS cc_start: 0.7824 (mtmm) cc_final: 0.7292 (mttp) REVERT: B 347 LYS cc_start: 0.6626 (mttp) cc_final: 0.5634 (mtmt) REVERT: C 17 LYS cc_start: 0.7270 (tttm) cc_final: 0.6589 (ttpt) REVERT: C 208 GLU cc_start: 0.6962 (mp0) cc_final: 0.6661 (mp0) REVERT: C 253 GLU cc_start: 0.7757 (tm-30) cc_final: 0.6584 (mt-10) REVERT: C 275 LYS cc_start: 0.7828 (mtmm) cc_final: 0.7298 (mttp) REVERT: C 347 LYS cc_start: 0.6615 (mttp) cc_final: 0.5669 (mtmt) REVERT: D 17 LYS cc_start: 0.7280 (tttm) cc_final: 0.6601 (ttpt) REVERT: D 208 GLU cc_start: 0.6964 (mp0) cc_final: 0.6657 (mp0) REVERT: D 253 GLU cc_start: 0.7765 (tm-30) cc_final: 0.6584 (mt-10) REVERT: D 275 LYS cc_start: 0.7839 (mtmm) cc_final: 0.7312 (mttp) REVERT: D 300 ASP cc_start: 0.8077 (m-30) cc_final: 0.7844 (m-30) REVERT: D 347 LYS cc_start: 0.6634 (mttp) cc_final: 0.5639 (mtmt) outliers start: 36 outliers final: 28 residues processed: 168 average time/residue: 0.5445 time to fit residues: 98.7852 Evaluate side-chains 162 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 313 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN B 147 GLN C 147 GLN D 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.130515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.104787 restraints weight = 9711.932| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.36 r_work: 0.2950 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10786 Z= 0.138 Angle : 0.493 7.955 14640 Z= 0.245 Chirality : 0.045 0.135 1624 Planarity : 0.003 0.030 1856 Dihedral : 5.777 38.441 1508 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.54 % Allowed : 23.51 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.74 (0.22), residues: 1380 helix: 0.45 (0.25), residues: 460 sheet: -1.24 (0.32), residues: 236 loop : -0.77 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 260 TYR 0.015 0.001 TYR A 258 PHE 0.012 0.001 PHE C 221 TRP 0.005 0.001 TRP B 54 HIS 0.001 0.000 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (10756) covalent geometry : angle 0.48877 / 0.24 (14612) SS BOND : bond 0.00129 / 0.06 ( 2) SS BOND : angle 0.41937 / 0.21 ( 4) hydrogen bonds : bond 0.03034 / 2.13 ( 400) hydrogen bonds : angle 4.88540 / 3.44 ( 1176) metal coordination : bond 0.00275 / 0.18 ( 28) metal coordination : angle 1.75563 / 1.16 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 0.393 Fit side-chains REVERT: A 17 LYS cc_start: 0.7329 (tttm) cc_final: 0.6646 (ttpt) REVERT: A 208 GLU cc_start: 0.6871 (mp0) cc_final: 0.6602 (mp0) REVERT: A 253 GLU cc_start: 0.7781 (tm-30) cc_final: 0.6593 (mt-10) REVERT: A 275 LYS cc_start: 0.7828 (mtmm) cc_final: 0.7258 (mttp) REVERT: A 314 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7273 (tptt) REVERT: A 347 LYS cc_start: 0.6695 (mttp) cc_final: 0.5688 (mtmt) REVERT: B 17 LYS cc_start: 0.7334 (tttm) cc_final: 0.6642 (ttpt) REVERT: B 208 GLU cc_start: 0.6883 (mp0) cc_final: 0.6613 (mp0) REVERT: B 253 GLU cc_start: 0.7773 (tm-30) cc_final: 0.6589 (mt-10) REVERT: B 275 LYS cc_start: 0.7797 (mtmm) cc_final: 0.7230 (mttp) REVERT: B 314 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7264 (tptt) REVERT: B 347 LYS cc_start: 0.6698 (mttp) cc_final: 0.5686 (mtmt) REVERT: C 17 LYS cc_start: 0.7319 (tttm) cc_final: 0.6628 (ttpt) REVERT: C 208 GLU cc_start: 0.6866 (mp0) cc_final: 0.6600 (mp0) REVERT: C 253 GLU cc_start: 0.7768 (tm-30) cc_final: 0.6581 (mt-10) REVERT: C 275 LYS cc_start: 0.7763 (mtmm) cc_final: 0.7272 (mttp) REVERT: C 347 LYS cc_start: 0.6680 (mttp) cc_final: 0.5689 (mtmt) REVERT: D 17 LYS cc_start: 0.7325 (tttm) cc_final: 0.6638 (ttpt) REVERT: D 208 GLU cc_start: 0.6867 (mp0) cc_final: 0.6595 (mp0) REVERT: D 253 GLU cc_start: 0.7765 (tm-30) cc_final: 0.6582 (mt-10) REVERT: D 275 LYS cc_start: 0.7775 (mtmm) cc_final: 0.7289 (mttp) REVERT: D 300 ASP cc_start: 0.8076 (m-30) cc_final: 0.7844 (m-30) REVERT: D 314 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7275 (tptt) REVERT: D 347 LYS cc_start: 0.6688 (mttp) cc_final: 0.5673 (mtmt) outliers start: 38 outliers final: 28 residues processed: 170 average time/residue: 0.5963 time to fit residues: 109.1221 Evaluate side-chains 163 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 314 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 37 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN B 147 GLN C 147 GLN D 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.128568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.102366 restraints weight = 9705.536| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.39 r_work: 0.2969 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10786 Z= 0.128 Angle : 0.488 8.338 14640 Z= 0.241 Chirality : 0.044 0.135 1624 Planarity : 0.003 0.031 1856 Dihedral : 5.686 38.422 1508 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.73 % Allowed : 23.79 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.66 (0.22), residues: 1380 helix: 0.54 (0.25), residues: 460 sheet: -1.24 (0.32), residues: 236 loop : -0.73 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 260 TYR 0.015 0.001 TYR D 258 PHE 0.011 0.001 PHE C 221 TRP 0.006 0.001 TRP B 54 HIS 0.001 0.000 HIS D 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (10756) covalent geometry : angle 0.48275 / 0.24 (14612) SS BOND : bond 0.00117 / 0.06 ( 2) SS BOND : angle 0.39366 / 0.20 ( 4) hydrogen bonds : bond 0.02962 / 2.09 ( 400) hydrogen bonds : angle 4.84220 / 3.41 ( 1176) metal coordination : bond 0.00212 / 0.14 ( 28) metal coordination : angle 1.76584 / 1.17 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.407 Fit side-chains REVERT: A 17 LYS cc_start: 0.7102 (tttm) cc_final: 0.6414 (ttpt) REVERT: A 208 GLU cc_start: 0.6884 (mp0) cc_final: 0.6559 (mp0) REVERT: A 253 GLU cc_start: 0.7811 (tm-30) cc_final: 0.6627 (mt-10) REVERT: A 275 LYS cc_start: 0.7776 (mtmm) cc_final: 0.7245 (mttp) REVERT: A 314 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7259 (tptt) REVERT: A 347 LYS cc_start: 0.6675 (mttp) cc_final: 0.5672 (mtmt) REVERT: B 17 LYS cc_start: 0.7095 (tttm) cc_final: 0.6396 (ttpt) REVERT: B 208 GLU cc_start: 0.6898 (mp0) cc_final: 0.6572 (mp0) REVERT: B 253 GLU cc_start: 0.7786 (tm-30) cc_final: 0.6608 (mt-10) REVERT: B 275 LYS cc_start: 0.7761 (mtmm) cc_final: 0.7239 (mttp) REVERT: B 314 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7259 (tptt) REVERT: B 347 LYS cc_start: 0.6687 (mttp) cc_final: 0.5675 (mtmt) REVERT: C 17 LYS cc_start: 0.7082 (tttm) cc_final: 0.6387 (ttpt) REVERT: C 208 GLU cc_start: 0.6910 (mp0) cc_final: 0.6584 (mp0) REVERT: C 253 GLU cc_start: 0.7781 (tm-30) cc_final: 0.6598 (mt-10) REVERT: C 275 LYS cc_start: 0.7760 (mtmm) cc_final: 0.7258 (mttp) REVERT: C 314 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7238 (tptt) REVERT: C 347 LYS cc_start: 0.6660 (mttp) cc_final: 0.5657 (mtmt) REVERT: D 17 LYS cc_start: 0.7090 (tttm) cc_final: 0.6397 (ttpt) REVERT: D 208 GLU cc_start: 0.6927 (mp0) cc_final: 0.6596 (mp0) REVERT: D 253 GLU cc_start: 0.7771 (tm-30) cc_final: 0.6598 (mt-10) REVERT: D 275 LYS cc_start: 0.7783 (mtmm) cc_final: 0.7285 (mttp) REVERT: D 300 ASP cc_start: 0.8075 (m-30) cc_final: 0.7846 (m-30) REVERT: D 314 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7252 (tptt) REVERT: D 347 LYS cc_start: 0.6683 (mttp) cc_final: 0.5670 (mtmt) outliers start: 40 outliers final: 28 residues processed: 168 average time/residue: 0.5655 time to fit residues: 102.5317 Evaluate side-chains 164 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 314 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 119 optimal weight: 6.9990 chunk 90 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN B 147 GLN C 147 GLN D 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.127291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.101520 restraints weight = 9828.477| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.34 r_work: 0.2927 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10786 Z= 0.179 Angle : 0.527 9.318 14640 Z= 0.259 Chirality : 0.046 0.135 1624 Planarity : 0.003 0.030 1856 Dihedral : 5.823 38.043 1508 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.08 % Allowed : 24.35 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.81 (0.22), residues: 1380 helix: 0.40 (0.25), residues: 460 sheet: -1.30 (0.31), residues: 260 loop : -0.78 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 340 TYR 0.016 0.001 TYR A 258 PHE 0.013 0.002 PHE D 221 TRP 0.006 0.001 TRP C 92 HIS 0.001 0.000 HIS D 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (10756) covalent geometry : angle 0.52082 / 0.26 (14612) SS BOND : bond 0.00190 / 0.09 ( 2) SS BOND : angle 0.47095 / 0.24 ( 4) hydrogen bonds : bond 0.03205 / 2.24 ( 400) hydrogen bonds : angle 4.97436 / 3.50 ( 1176) metal coordination : bond 0.00458 / 0.31 ( 28) metal coordination : angle 2.07505 / 1.37 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3340.13 seconds wall clock time: 58 minutes 6.67 seconds (3486.67 seconds total)