Starting phenix.real_space_refine on Wed Mar 4 03:37:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kcb_22807/03_2026/7kcb_22807.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kcb_22807/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7kcb_22807/03_2026/7kcb_22807.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kcb_22807/03_2026/7kcb_22807.map" model { file = "/net/cci-nas-00/data/ceres_data/7kcb_22807/03_2026/7kcb_22807.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kcb_22807/03_2026/7kcb_22807.cif" } 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-5986/lib/python3.9/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: 2.09, per 1000 atoms: 0.20 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: 0.90 Conformation dependent library (CDL) restraints added in 534.8 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: 0.44 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: 1.75 Time building geometry restraints manager: 1.18 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: 5470 16.66 - 33.33: 644 33.33 - 49.99: 216 49.99 - 66.65: 64 66.65 - 83.31: 12 Dihedral angle restraints: 6406 sinusoidal: 2542 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 6403 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.950 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 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 : 17.035 83.309 3976 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 covalent geometry : bond 0.01117 (10756) covalent geometry : angle 0.90995 (14612) SS BOND : bond 0.06347 ( 2) SS BOND : angle 1.70741 ( 4) hydrogen bonds : bond 0.16409 ( 400) hydrogen bonds : angle 8.51356 ( 1176) metal coordination : bond 0.12421 ( 28) metal coordination : angle 7.20305 ( 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 : 0.402 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: 0.5847 time to fit residues: 110.6583 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 : 0.367 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3452 r_free = 0.3452 target = 0.133172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.107570 restraints weight = 9654.659| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.34 r_work: 0.2983 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1558 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= 0.119 Angle : 0.495 4.756 14640 Z= 0.254 Chirality : 0.045 0.137 1624 Planarity : 0.004 0.046 1856 Dihedral : 9.259 57.941 1736 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.24 % Allowed : 21.64 % Favored : 76.12 % 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: -1.77 (0.20), residues: 1380 helix: -0.48 (0.24), residues: 452 sheet: -1.41 (0.30), residues: 240 loop : -1.51 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 310 TYR 0.015 0.001 TYR B 258 PHE 0.011 0.001 PHE B 221 TRP 0.003 0.001 TRP A 54 HIS 0.003 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00266 (10756) covalent geometry : angle 0.48833 (14612) SS BOND : bond 0.00148 ( 2) SS BOND : angle 0.89471 ( 4) hydrogen bonds : bond 0.03322 ( 400) hydrogen bonds : angle 5.56490 ( 1176) metal coordination : bond 0.00524 ( 28) metal coordination : angle 2.01211 ( 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 : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 THR cc_start: 0.8350 (OUTLIER) cc_final: 0.8003 (t) REVERT: A 17 LYS cc_start: 0.6512 (tttm) cc_final: 0.5806 (ttpt) REVERT: A 208 GLU cc_start: 0.7027 (mp0) cc_final: 0.6771 (mp0) REVERT: A 275 LYS cc_start: 0.7904 (mtmm) cc_final: 0.7424 (mttp) REVERT: A 300 ASP cc_start: 0.8082 (m-30) cc_final: 0.7797 (m-30) REVERT: B 5 THR cc_start: 0.8362 (OUTLIER) cc_final: 0.8019 (t) REVERT: B 17 LYS cc_start: 0.6501 (tttm) cc_final: 0.5807 (ttpt) REVERT: B 208 GLU cc_start: 0.7021 (mp0) cc_final: 0.6766 (mp0) REVERT: B 275 LYS cc_start: 0.7912 (mtmm) cc_final: 0.7430 (mttp) REVERT: B 300 ASP cc_start: 0.8063 (m-30) cc_final: 0.7773 (m-30) REVERT: C 5 THR cc_start: 0.8358 (OUTLIER) cc_final: 0.8014 (t) REVERT: C 17 LYS cc_start: 0.6516 (tttm) cc_final: 0.5807 (ttpt) REVERT: C 208 GLU cc_start: 0.7034 (mp0) cc_final: 0.6779 (mp0) REVERT: C 275 LYS cc_start: 0.7907 (mtmm) cc_final: 0.7436 (mttp) REVERT: C 300 ASP cc_start: 0.8059 (m-30) cc_final: 0.7771 (m-30) REVERT: D 5 THR cc_start: 0.8349 (OUTLIER) cc_final: 0.8004 (t) REVERT: D 17 LYS cc_start: 0.6535 (tttm) cc_final: 0.5839 (ttpt) REVERT: D 208 GLU cc_start: 0.7044 (mp0) cc_final: 0.6786 (mp0) REVERT: D 275 LYS cc_start: 0.7914 (mtmm) cc_final: 0.7439 (mttp) REVERT: D 300 ASP cc_start: 0.8144 (m-30) cc_final: 0.7863 (m-30) outliers start: 24 outliers final: 8 residues processed: 152 average time/residue: 0.6089 time to fit residues: 99.3951 Evaluate side-chains 130 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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: 9.9990 chunk 62 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3365 r_free = 0.3365 target = 0.125620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.099802 restraints weight = 9828.827| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.35 r_work: 0.2894 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 10786 Z= 0.276 Angle : 0.606 6.886 14640 Z= 0.303 Chirality : 0.049 0.137 1624 Planarity : 0.004 0.038 1856 Dihedral : 9.725 58.364 1708 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.73 % Allowed : 22.01 % 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: -1.51 (0.21), residues: 1380 helix: -0.45 (0.24), residues: 456 sheet: -1.07 (0.32), residues: 236 loop : -1.30 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 310 TYR 0.018 0.002 TYR C 258 PHE 0.012 0.002 PHE B 221 TRP 0.010 0.002 TRP A 92 HIS 0.003 0.001 HIS B 48 Details of bonding type rmsd covalent geometry : bond 0.00656 (10756) covalent geometry : angle 0.59591 (14612) SS BOND : bond 0.00311 ( 2) SS BOND : angle 1.20421 ( 4) hydrogen bonds : bond 0.03972 ( 400) hydrogen bonds : angle 5.58189 ( 1176) metal coordination : bond 0.00746 ( 28) metal coordination : angle 2.71783 ( 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 175 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 0.365 Fit side-chains REVERT: A 5 THR cc_start: 0.8306 (OUTLIER) cc_final: 0.8016 (t) REVERT: A 17 LYS cc_start: 0.6932 (tttm) cc_final: 0.6235 (ttpt) REVERT: A 182 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8314 (mp) REVERT: A 208 GLU cc_start: 0.6964 (mp0) cc_final: 0.6660 (mp0) REVERT: A 275 LYS cc_start: 0.8015 (mtmm) cc_final: 0.7485 (mttp) REVERT: A 300 ASP cc_start: 0.8207 (m-30) cc_final: 0.7961 (m-30) REVERT: A 347 LYS cc_start: 0.6875 (mttm) cc_final: 0.6626 (mttp) REVERT: B 5 THR cc_start: 0.8315 (OUTLIER) cc_final: 0.8021 (t) REVERT: B 17 LYS cc_start: 0.6942 (tttm) cc_final: 0.6234 (ttpt) REVERT: B 182 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8321 (mp) REVERT: B 208 GLU cc_start: 0.6998 (mp0) cc_final: 0.6695 (mp0) REVERT: B 275 LYS cc_start: 0.8003 (mtmm) cc_final: 0.7479 (mttp) REVERT: B 300 ASP cc_start: 0.8197 (m-30) cc_final: 0.7946 (m-30) REVERT: B 347 LYS cc_start: 0.6881 (mttm) cc_final: 0.6629 (mttp) REVERT: C 5 THR cc_start: 0.8311 (OUTLIER) cc_final: 0.8019 (t) REVERT: C 17 LYS cc_start: 0.6940 (tttm) cc_final: 0.6237 (ttpt) REVERT: C 182 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8326 (mp) REVERT: C 208 GLU cc_start: 0.7004 (mp0) cc_final: 0.6703 (mp0) REVERT: C 275 LYS cc_start: 0.8011 (mtmm) cc_final: 0.7480 (mttp) REVERT: C 277 CYS cc_start: 0.7888 (m) cc_final: 0.7657 (m) REVERT: C 300 ASP cc_start: 0.8198 (m-30) cc_final: 0.7948 (m-30) REVERT: C 347 LYS cc_start: 0.6894 (mttm) cc_final: 0.6635 (mttp) REVERT: D 5 THR cc_start: 0.8310 (OUTLIER) cc_final: 0.8018 (t) REVERT: D 17 LYS cc_start: 0.6940 (tttm) cc_final: 0.6239 (ttpt) REVERT: D 182 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8324 (mp) REVERT: D 208 GLU cc_start: 0.7005 (mp0) cc_final: 0.6699 (mp0) REVERT: D 275 LYS cc_start: 0.8008 (mtmm) cc_final: 0.7489 (mttp) REVERT: D 277 CYS cc_start: 0.7895 (m) cc_final: 0.7670 (m) REVERT: D 300 ASP cc_start: 0.8203 (m-30) cc_final: 0.7955 (m-30) REVERT: D 347 LYS cc_start: 0.6882 (mttm) cc_final: 0.6620 (mttp) outliers start: 40 outliers final: 25 residues processed: 171 average time/residue: 0.5297 time to fit residues: 98.0513 Evaluate side-chains 163 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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: 2.9990 chunk 106 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3423 r_free = 0.3423 target = 0.130681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.105098 restraints weight = 9817.019| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.35 r_work: 0.2962 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10786 Z= 0.130 Angle : 0.482 5.195 14640 Z= 0.244 Chirality : 0.044 0.140 1624 Planarity : 0.004 0.032 1856 Dihedral : 9.205 57.111 1708 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.82 % Allowed : 21.92 % 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: -1.14 (0.21), residues: 1380 helix: 0.07 (0.25), residues: 456 sheet: -1.21 (0.32), residues: 240 loop : -1.08 (0.21), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 260 TYR 0.016 0.001 TYR B 258 PHE 0.011 0.001 PHE C 221 TRP 0.003 0.001 TRP B 92 HIS 0.001 0.000 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00299 (10756) covalent geometry : angle 0.47626 (14612) SS BOND : bond 0.00072 ( 2) SS BOND : angle 0.65091 ( 4) hydrogen bonds : bond 0.03205 ( 400) hydrogen bonds : angle 5.06896 ( 1176) metal coordination : bond 0.00196 ( 28) metal coordination : angle 1.90144 ( 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 179 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 138 time to evaluate : 0.363 Fit side-chains REVERT: A 5 THR cc_start: 0.8252 (OUTLIER) cc_final: 0.7987 (t) REVERT: A 17 LYS cc_start: 0.6930 (tttm) cc_final: 0.6220 (ttpt) REVERT: A 77 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7394 (mt-10) REVERT: A 208 GLU cc_start: 0.6903 (mp0) cc_final: 0.6600 (mp0) REVERT: A 275 LYS cc_start: 0.7957 (mtmm) cc_final: 0.7484 (mttp) REVERT: A 300 ASP cc_start: 0.8119 (m-30) cc_final: 0.7878 (m-30) REVERT: A 347 LYS cc_start: 0.6612 (OUTLIER) cc_final: 0.5817 (mtmt) REVERT: B 5 THR cc_start: 0.8261 (OUTLIER) cc_final: 0.7993 (t) REVERT: B 17 LYS cc_start: 0.6961 (tttm) cc_final: 0.6240 (ttpt) REVERT: B 77 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7373 (mt-10) REVERT: B 208 GLU cc_start: 0.6931 (mp0) cc_final: 0.6630 (mp0) REVERT: B 275 LYS cc_start: 0.7942 (mtmm) cc_final: 0.7473 (mttp) REVERT: B 300 ASP cc_start: 0.8111 (m-30) cc_final: 0.7867 (m-30) REVERT: B 347 LYS cc_start: 0.6582 (OUTLIER) cc_final: 0.5795 (mtmt) REVERT: C 5 THR cc_start: 0.8264 (OUTLIER) cc_final: 0.7999 (t) REVERT: C 17 LYS cc_start: 0.6941 (tttm) cc_final: 0.6224 (ttpt) REVERT: C 77 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7363 (mt-10) REVERT: C 208 GLU cc_start: 0.6937 (mp0) cc_final: 0.6634 (mp0) REVERT: C 275 LYS cc_start: 0.7958 (mtmm) cc_final: 0.7467 (mttp) REVERT: C 277 CYS cc_start: 0.7807 (m) cc_final: 0.7575 (m) REVERT: C 300 ASP cc_start: 0.8108 (m-30) cc_final: 0.7860 (m-30) REVERT: C 347 LYS cc_start: 0.6584 (mttm) cc_final: 0.5796 (mtmt) REVERT: D 5 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.7998 (t) REVERT: D 17 LYS cc_start: 0.6956 (tttm) cc_final: 0.6239 (ttpt) REVERT: D 77 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7350 (mt-10) REVERT: D 208 GLU cc_start: 0.6940 (mp0) cc_final: 0.6634 (mp0) REVERT: D 253 GLU cc_start: 0.7860 (tm-30) cc_final: 0.6767 (mt-10) REVERT: D 275 LYS cc_start: 0.7966 (mtmm) cc_final: 0.7400 (mttp) REVERT: D 277 CYS cc_start: 0.7824 (m) cc_final: 0.7605 (m) REVERT: D 300 ASP cc_start: 0.8117 (m-30) cc_final: 0.7868 (m-30) REVERT: D 347 LYS cc_start: 0.6576 (mttm) cc_final: 0.5786 (mtmt) outliers start: 41 outliers final: 15 residues processed: 169 average time/residue: 0.5438 time to fit residues: 99.4837 Evaluate side-chains 158 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 A residue 313 VAL Chi-restraints excluded: chain A residue 347 LYS 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 B residue 347 LYS 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 C residue 313 VAL 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 Chi-restraints excluded: chain D residue 313 VAL 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: 0.9980 chunk 65 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 104 optimal weight: 0.1980 chunk 42 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3367 r_free = 0.3367 target = 0.126191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.100463 restraints weight = 9783.860| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.33 r_work: 0.2920 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10786 Z= 0.211 Angle : 0.534 5.317 14640 Z= 0.268 Chirality : 0.046 0.138 1624 Planarity : 0.004 0.031 1856 Dihedral : 9.488 57.269 1708 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.85 % Allowed : 22.39 % 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: -1.17 (0.21), residues: 1380 helix: -0.02 (0.24), residues: 456 sheet: -1.19 (0.31), residues: 260 loop : -1.05 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 340 TYR 0.016 0.001 TYR A 258 PHE 0.014 0.002 PHE D 221 TRP 0.008 0.001 TRP D 92 HIS 0.002 0.000 HIS C 240 Details of bonding type rmsd covalent geometry : bond 0.00502 (10756) covalent geometry : angle 0.52691 (14612) SS BOND : bond 0.00164 ( 2) SS BOND : angle 0.61712 ( 4) hydrogen bonds : bond 0.03515 ( 400) hydrogen bonds : angle 5.17166 ( 1176) metal coordination : bond 0.00523 ( 28) metal coordination : angle 2.19445 ( 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 186 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 134 time to evaluate : 0.392 Fit side-chains REVERT: A 5 THR cc_start: 0.8308 (OUTLIER) cc_final: 0.8101 (t) REVERT: A 17 LYS cc_start: 0.7241 (tttm) cc_final: 0.6549 (ttpt) REVERT: A 182 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8411 (mp) REVERT: A 208 GLU cc_start: 0.6855 (mp0) cc_final: 0.6531 (mp0) REVERT: A 253 GLU cc_start: 0.7877 (tm-30) cc_final: 0.6781 (mt-10) REVERT: A 275 LYS cc_start: 0.8016 (mtmm) cc_final: 0.7417 (mttp) REVERT: A 300 ASP cc_start: 0.8154 (m-30) cc_final: 0.7898 (m-30) REVERT: A 347 LYS cc_start: 0.6672 (OUTLIER) cc_final: 0.5955 (mtmt) REVERT: B 5 THR cc_start: 0.8313 (OUTLIER) cc_final: 0.8104 (t) REVERT: B 17 LYS cc_start: 0.7245 (tttm) cc_final: 0.6546 (ttpt) REVERT: B 182 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8407 (mp) REVERT: B 208 GLU cc_start: 0.6883 (mp0) cc_final: 0.6561 (mp0) REVERT: B 253 GLU cc_start: 0.7862 (tm-30) cc_final: 0.6763 (mt-10) REVERT: B 275 LYS cc_start: 0.8003 (mtmm) cc_final: 0.7414 (mttp) REVERT: B 300 ASP cc_start: 0.8143 (m-30) cc_final: 0.7878 (m-30) REVERT: B 347 LYS cc_start: 0.6668 (OUTLIER) cc_final: 0.5947 (mtmt) REVERT: C 5 THR cc_start: 0.8307 (OUTLIER) cc_final: 0.8099 (t) REVERT: C 17 LYS cc_start: 0.7229 (tttm) cc_final: 0.6531 (ttpt) REVERT: C 182 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8405 (mp) REVERT: C 208 GLU cc_start: 0.6887 (mp0) cc_final: 0.6562 (mp0) REVERT: C 253 GLU cc_start: 0.7869 (tm-30) cc_final: 0.6766 (mt-10) REVERT: C 275 LYS cc_start: 0.8000 (mtmm) cc_final: 0.7405 (mttp) REVERT: C 300 ASP cc_start: 0.8157 (m-30) cc_final: 0.7899 (m-30) REVERT: C 347 LYS cc_start: 0.6688 (OUTLIER) cc_final: 0.5971 (mtmt) REVERT: D 5 THR cc_start: 0.8312 (OUTLIER) cc_final: 0.8107 (t) REVERT: D 17 LYS cc_start: 0.7241 (tttm) cc_final: 0.6499 (ttpt) REVERT: D 182 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8260 (mp) REVERT: D 208 GLU cc_start: 0.6881 (mp0) cc_final: 0.6549 (mp0) REVERT: D 253 GLU cc_start: 0.7848 (tm-30) cc_final: 0.6761 (mt-10) REVERT: D 275 LYS cc_start: 0.8021 (mtmm) cc_final: 0.7434 (mttp) REVERT: D 300 ASP cc_start: 0.8134 (m-30) cc_final: 0.7869 (m-30) REVERT: D 347 LYS cc_start: 0.6690 (OUTLIER) cc_final: 0.5969 (mtmt) outliers start: 52 outliers final: 27 residues processed: 170 average time/residue: 0.5353 time to fit residues: 98.4426 Evaluate side-chains 174 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 58 VAL Chi-restraints excluded: chain A residue 182 LEU 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 A residue 347 LYS 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 58 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 347 LYS 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 58 VAL Chi-restraints excluded: chain C residue 182 LEU 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 C residue 347 LYS 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 58 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 347 LYS 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: 7.9990 chunk 104 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3385 r_free = 0.3385 target = 0.127860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.101913 restraints weight = 9869.042| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.35 r_work: 0.2935 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10786 Z= 0.158 Angle : 0.499 5.142 14640 Z= 0.251 Chirality : 0.045 0.135 1624 Planarity : 0.003 0.032 1856 Dihedral : 9.330 56.617 1708 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.48 % Allowed : 21.74 % Favored : 73.79 % 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: -1.08 (0.21), residues: 1380 helix: 0.09 (0.24), residues: 460 sheet: -1.26 (0.31), residues: 260 loop : -0.97 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 260 TYR 0.016 0.001 TYR B 258 PHE 0.013 0.002 PHE B 221 TRP 0.005 0.001 TRP A 92 HIS 0.001 0.000 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00372 (10756) covalent geometry : angle 0.49311 (14612) SS BOND : bond 0.00140 ( 2) SS BOND : angle 0.50160 ( 4) hydrogen bonds : bond 0.03222 ( 400) hydrogen bonds : angle 5.03840 ( 1176) metal coordination : bond 0.00317 ( 28) metal coordination : angle 1.98685 ( 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 183 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 135 time to evaluate : 0.470 Fit side-chains REVERT: A 17 LYS cc_start: 0.7268 (tttm) cc_final: 0.6578 (ttpt) REVERT: A 182 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8388 (mp) REVERT: A 208 GLU cc_start: 0.6835 (mp0) cc_final: 0.6554 (mp0) REVERT: A 253 GLU cc_start: 0.7778 (tm-30) cc_final: 0.6613 (mt-10) REVERT: A 275 LYS cc_start: 0.7906 (mtmm) cc_final: 0.7321 (mttp) REVERT: A 300 ASP cc_start: 0.8130 (m-30) cc_final: 0.7879 (m-30) REVERT: A 347 LYS cc_start: 0.6669 (OUTLIER) cc_final: 0.5934 (mtmt) REVERT: B 17 LYS cc_start: 0.7248 (tttm) cc_final: 0.6574 (ttpt) REVERT: B 182 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8379 (mp) REVERT: B 208 GLU cc_start: 0.6855 (mp0) cc_final: 0.6580 (mp0) REVERT: B 253 GLU cc_start: 0.7804 (tm-30) cc_final: 0.6688 (mt-10) REVERT: B 275 LYS cc_start: 0.7955 (mtmm) cc_final: 0.7323 (mttp) REVERT: B 300 ASP cc_start: 0.8119 (m-30) cc_final: 0.7871 (m-30) REVERT: B 347 LYS cc_start: 0.6652 (OUTLIER) cc_final: 0.5912 (mtmt) REVERT: C 17 LYS cc_start: 0.7261 (tttm) cc_final: 0.6565 (ttpt) REVERT: C 182 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8380 (mp) REVERT: C 208 GLU cc_start: 0.6856 (mp0) cc_final: 0.6577 (mp0) REVERT: C 253 GLU cc_start: 0.7765 (tm-30) cc_final: 0.6594 (mt-10) REVERT: C 275 LYS cc_start: 0.8007 (mtmm) cc_final: 0.7386 (mttp) REVERT: C 300 ASP cc_start: 0.8119 (m-30) cc_final: 0.7866 (m-30) REVERT: C 347 LYS cc_start: 0.6665 (OUTLIER) cc_final: 0.5763 (mtmt) REVERT: D 17 LYS cc_start: 0.7242 (tttm) cc_final: 0.6521 (ttpt) REVERT: D 182 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8383 (mp) REVERT: D 208 GLU cc_start: 0.6857 (mp0) cc_final: 0.6583 (mp0) REVERT: D 253 GLU cc_start: 0.7757 (tm-30) cc_final: 0.6596 (mt-10) REVERT: D 275 LYS cc_start: 0.8029 (mtmm) cc_final: 0.7414 (mttp) REVERT: D 300 ASP cc_start: 0.8127 (m-30) cc_final: 0.7882 (m-30) REVERT: D 312 LEU cc_start: 0.9040 (mt) cc_final: 0.8834 (mt) REVERT: D 347 LYS cc_start: 0.6673 (OUTLIER) cc_final: 0.5776 (mtmt) outliers start: 48 outliers final: 21 residues processed: 169 average time/residue: 0.5433 time to fit residues: 99.4342 Evaluate side-chains 162 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 182 LEU 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 A residue 347 LYS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 182 LEU 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 347 LYS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 347 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 116 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3404 r_free = 0.3404 target = 0.129632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.103869 restraints weight = 9747.815| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.34 r_work: 0.2963 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2248 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 : 0.473 5.413 14640 Z= 0.238 Chirality : 0.044 0.136 1624 Planarity : 0.003 0.032 1856 Dihedral : 9.125 58.874 1708 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.45 % Allowed : 22.76 % Favored : 73.79 % 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: -0.80 (0.22), residues: 1380 helix: 0.34 (0.24), residues: 460 sheet: -1.23 (0.33), residues: 236 loop : -0.78 (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 A 258 PHE 0.011 0.001 PHE A 221 TRP 0.005 0.001 TRP D 54 HIS 0.001 0.000 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00297 (10756) covalent geometry : angle 0.46805 (14612) SS BOND : bond 0.00113 ( 2) SS BOND : angle 0.42529 ( 4) hydrogen bonds : bond 0.03016 ( 400) hydrogen bonds : angle 4.88560 ( 1176) metal coordination : bond 0.00212 ( 28) metal coordination : angle 1.76257 ( 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 175 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.393 Fit side-chains REVERT: A 17 LYS cc_start: 0.7256 (tttm) cc_final: 0.6588 (ttpt) REVERT: A 208 GLU cc_start: 0.6776 (mp0) cc_final: 0.6527 (mp0) REVERT: A 253 GLU cc_start: 0.7806 (tm-30) cc_final: 0.6617 (mt-10) REVERT: A 275 LYS cc_start: 0.7901 (mtmm) cc_final: 0.7388 (mttp) REVERT: A 300 ASP cc_start: 0.8085 (m-30) cc_final: 0.7850 (m-30) REVERT: A 347 LYS cc_start: 0.6646 (OUTLIER) cc_final: 0.5705 (mtmt) REVERT: B 17 LYS cc_start: 0.7303 (tttm) cc_final: 0.6610 (ttpt) REVERT: B 208 GLU cc_start: 0.6906 (mp0) cc_final: 0.6646 (mp0) REVERT: B 253 GLU cc_start: 0.7783 (tm-30) cc_final: 0.6596 (mt-10) REVERT: B 275 LYS cc_start: 0.7884 (mtmm) cc_final: 0.7380 (mttp) REVERT: B 300 ASP cc_start: 0.8084 (m-30) cc_final: 0.7850 (m-30) REVERT: B 347 LYS cc_start: 0.6604 (OUTLIER) cc_final: 0.5663 (mtmt) REVERT: C 17 LYS cc_start: 0.7298 (tttm) cc_final: 0.6601 (ttpt) REVERT: C 208 GLU cc_start: 0.6895 (mp0) cc_final: 0.6621 (mp0) REVERT: C 253 GLU cc_start: 0.7766 (tm-30) cc_final: 0.6594 (mt-10) REVERT: C 275 LYS cc_start: 0.7814 (mtmm) cc_final: 0.7297 (mttp) REVERT: C 300 ASP cc_start: 0.8075 (m-30) cc_final: 0.7835 (m-30) REVERT: C 347 LYS cc_start: 0.6648 (mttm) cc_final: 0.5719 (mtmt) REVERT: D 17 LYS cc_start: 0.7254 (tttm) cc_final: 0.6589 (ttpt) REVERT: D 208 GLU cc_start: 0.6885 (mp0) cc_final: 0.6589 (mp0) REVERT: D 253 GLU cc_start: 0.7791 (tm-30) cc_final: 0.6598 (mt-10) REVERT: D 275 LYS cc_start: 0.7828 (mtmm) cc_final: 0.7314 (mttp) REVERT: D 300 ASP cc_start: 0.8080 (m-30) cc_final: 0.7846 (m-30) REVERT: D 347 LYS cc_start: 0.6655 (mttm) cc_final: 0.5718 (mtmt) outliers start: 37 outliers final: 20 residues processed: 173 average time/residue: 0.5889 time to fit residues: 109.6566 Evaluate side-chains 149 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 247 VAL Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 33 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 347 LYS Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 33 LEU 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 247 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: 1.9990 chunk 92 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN B 121 HIS B 147 GLN C 121 HIS C 147 GLN D 147 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.125625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.099862 restraints weight = 9751.333| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.35 r_work: 0.2883 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2113 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= 0.293 Angle : 0.608 6.907 14640 Z= 0.301 Chirality : 0.049 0.145 1624 Planarity : 0.004 0.028 1856 Dihedral : 9.782 58.145 1708 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.82 % Allowed : 22.48 % Favored : 73.69 % 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: -1.14 (0.21), residues: 1380 helix: -0.03 (0.24), residues: 464 sheet: -1.21 (0.31), residues: 260 loop : -0.99 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 340 TYR 0.017 0.002 TYR D 258 PHE 0.014 0.002 PHE B 221 TRP 0.012 0.002 TRP C 92 HIS 0.002 0.001 HIS D 48 Details of bonding type rmsd covalent geometry : bond 0.00702 (10756) covalent geometry : angle 0.59778 (14612) SS BOND : bond 0.00246 ( 2) SS BOND : angle 0.63284 ( 4) hydrogen bonds : bond 0.03801 ( 400) hydrogen bonds : angle 5.25018 ( 1176) metal coordination : bond 0.00843 ( 28) metal coordination : angle 2.83166 ( 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 180 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 139 time to evaluate : 0.337 Fit side-chains REVERT: A 17 LYS cc_start: 0.7352 (tttm) cc_final: 0.6643 (ttpt) REVERT: A 182 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8340 (mp) REVERT: A 208 GLU cc_start: 0.6855 (mp0) cc_final: 0.6448 (mp0) REVERT: A 253 GLU cc_start: 0.7904 (tm-30) cc_final: 0.6834 (mt-10) REVERT: A 275 LYS cc_start: 0.7930 (mtmm) cc_final: 0.7335 (mttp) REVERT: A 300 ASP cc_start: 0.8170 (m-30) cc_final: 0.7903 (m-30) REVERT: A 314 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7357 (tptt) REVERT: B 17 LYS cc_start: 0.7356 (tttm) cc_final: 0.6631 (ttpt) REVERT: B 182 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8332 (mp) REVERT: B 208 GLU cc_start: 0.6875 (mp0) cc_final: 0.6468 (mp0) REVERT: B 253 GLU cc_start: 0.7889 (tm-30) cc_final: 0.6817 (mt-10) REVERT: B 275 LYS cc_start: 0.7930 (mtmm) cc_final: 0.7331 (mttp) REVERT: B 300 ASP cc_start: 0.8161 (m-30) cc_final: 0.7897 (m-30) REVERT: C 17 LYS cc_start: 0.7356 (tttm) cc_final: 0.6630 (ttpt) REVERT: C 182 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8342 (mp) REVERT: C 208 GLU cc_start: 0.6870 (mp0) cc_final: 0.6463 (mp0) REVERT: C 253 GLU cc_start: 0.7915 (tm-30) cc_final: 0.6834 (mt-10) REVERT: C 275 LYS cc_start: 0.7936 (mtmm) cc_final: 0.7343 (mttp) REVERT: C 300 ASP cc_start: 0.8168 (m-30) cc_final: 0.7901 (m-30) REVERT: C 347 LYS cc_start: 0.6676 (OUTLIER) cc_final: 0.5752 (mtmt) REVERT: D 17 LYS cc_start: 0.7336 (tttm) cc_final: 0.6631 (ttpt) REVERT: D 182 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8336 (mp) REVERT: D 208 GLU cc_start: 0.6872 (mp0) cc_final: 0.6465 (mp0) REVERT: D 253 GLU cc_start: 0.7892 (tm-30) cc_final: 0.6832 (mt-10) REVERT: D 275 LYS cc_start: 0.7942 (mtmm) cc_final: 0.7356 (mttp) REVERT: D 300 ASP cc_start: 0.8168 (m-30) cc_final: 0.7906 (m-30) REVERT: D 314 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7370 (tptt) REVERT: D 347 LYS cc_start: 0.6724 (OUTLIER) cc_final: 0.5807 (mtmt) outliers start: 41 outliers final: 28 residues processed: 172 average time/residue: 0.5551 time to fit residues: 103.2811 Evaluate side-chains 173 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 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 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 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 13 GLU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 58 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 C residue 347 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 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 Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 347 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 chunk 55 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 147 GLN B 147 GLN C 147 GLN D 121 HIS D 147 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.131291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.105602 restraints weight = 9717.809| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.35 r_work: 0.2974 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10786 Z= 0.114 Angle : 0.486 7.730 14640 Z= 0.241 Chirality : 0.044 0.134 1624 Planarity : 0.003 0.030 1856 Dihedral : 9.110 58.656 1708 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.99 % Allowed : 24.35 % Favored : 72.67 % 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: -0.75 (0.22), residues: 1380 helix: 0.43 (0.25), residues: 460 sheet: -1.30 (0.32), residues: 240 loop : -0.74 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 310 TYR 0.015 0.001 TYR D 258 PHE 0.011 0.001 PHE A 221 TRP 0.008 0.001 TRP D 54 HIS 0.002 0.000 HIS C 138 Details of bonding type rmsd covalent geometry : bond 0.00264 (10756) covalent geometry : angle 0.48027 (14612) SS BOND : bond 0.00121 ( 2) SS BOND : angle 0.45017 ( 4) hydrogen bonds : bond 0.02949 ( 400) hydrogen bonds : angle 4.86676 ( 1176) metal coordination : bond 0.00165 ( 28) metal coordination : angle 1.84683 ( 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 173 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.396 Fit side-chains REVERT: A 17 LYS cc_start: 0.7196 (tttm) cc_final: 0.6508 (ttpt) REVERT: A 208 GLU cc_start: 0.6851 (mp0) cc_final: 0.6501 (mp0) REVERT: A 253 GLU cc_start: 0.7812 (tm-30) cc_final: 0.6618 (mt-10) REVERT: A 275 LYS cc_start: 0.7817 (mtmm) cc_final: 0.7278 (mttp) REVERT: A 300 ASP cc_start: 0.8088 (m-30) cc_final: 0.7858 (m-30) REVERT: A 314 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7208 (tptt) REVERT: A 347 LYS cc_start: 0.6736 (mttp) cc_final: 0.5738 (mtmt) REVERT: B 17 LYS cc_start: 0.7347 (tttm) cc_final: 0.6662 (ttpt) REVERT: B 208 GLU cc_start: 0.6862 (mp0) cc_final: 0.6519 (mp0) REVERT: B 253 GLU cc_start: 0.7793 (tm-30) cc_final: 0.6611 (mt-10) REVERT: B 275 LYS cc_start: 0.7792 (mtmm) cc_final: 0.7256 (mttp) REVERT: B 300 ASP cc_start: 0.8089 (m-30) cc_final: 0.7863 (m-30) REVERT: B 314 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7196 (tptt) REVERT: B 347 LYS cc_start: 0.6704 (mttp) cc_final: 0.5674 (mtmt) REVERT: C 17 LYS cc_start: 0.7288 (tttm) cc_final: 0.6611 (ttpt) REVERT: C 208 GLU cc_start: 0.6859 (mp0) cc_final: 0.6508 (mp0) REVERT: C 253 GLU cc_start: 0.7789 (tm-30) cc_final: 0.6594 (mt-10) REVERT: C 275 LYS cc_start: 0.7811 (mtmm) cc_final: 0.7278 (mttp) REVERT: C 300 ASP cc_start: 0.8074 (m-30) cc_final: 0.7846 (m-30) REVERT: C 314 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7209 (tptt) REVERT: C 347 LYS cc_start: 0.6640 (mttm) cc_final: 0.5591 (mtmt) REVERT: D 17 LYS cc_start: 0.7306 (tttm) cc_final: 0.6631 (ttpt) REVERT: D 208 GLU cc_start: 0.6875 (mp0) cc_final: 0.6521 (mp0) REVERT: D 253 GLU cc_start: 0.7777 (tm-30) cc_final: 0.6591 (mt-10) REVERT: D 275 LYS cc_start: 0.7825 (mtmm) cc_final: 0.7289 (mttp) REVERT: D 300 ASP cc_start: 0.8085 (m-30) cc_final: 0.7862 (m-30) REVERT: D 314 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7207 (tptt) REVERT: D 347 LYS cc_start: 0.6667 (mttm) cc_final: 0.5612 (mtmt) outliers start: 32 outliers final: 26 residues processed: 173 average time/residue: 0.6113 time to fit residues: 113.6588 Evaluate side-chains 167 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 245 VAL Chi-restraints excluded: chain A residue 289 SER 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 245 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 289 SER 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 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 247 VAL Chi-restraints excluded: chain C residue 289 SER 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 247 VAL Chi-restraints excluded: chain D residue 289 SER 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: 0.9980 chunk 133 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 90 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3396 r_free = 0.3396 target = 0.128608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.102881 restraints weight = 9705.588| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.33 r_work: 0.2943 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10786 Z= 0.153 Angle : 0.509 8.217 14640 Z= 0.251 Chirality : 0.045 0.135 1624 Planarity : 0.003 0.030 1856 Dihedral : 9.297 59.755 1708 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.43 % Allowed : 24.91 % Favored : 72.67 % 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: 0.43 (0.25), residues: 460 sheet: -1.34 (0.31), residues: 260 loop : -0.80 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 211 TYR 0.016 0.001 TYR D 258 PHE 0.012 0.001 PHE A 221 TRP 0.006 0.001 TRP B 54 HIS 0.001 0.000 HIS D 121 Details of bonding type rmsd covalent geometry : bond 0.00359 (10756) covalent geometry : angle 0.50368 (14612) SS BOND : bond 0.00162 ( 2) SS BOND : angle 0.47239 ( 4) hydrogen bonds : bond 0.03101 ( 400) hydrogen bonds : angle 4.90647 ( 1176) metal coordination : bond 0.00341 ( 28) metal coordination : angle 1.95277 ( 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 167 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.393 Fit side-chains REVERT: A 17 LYS cc_start: 0.7205 (tttm) cc_final: 0.6506 (ttpt) REVERT: A 208 GLU cc_start: 0.6907 (mp0) cc_final: 0.6601 (mp0) REVERT: A 253 GLU cc_start: 0.7802 (tm-30) cc_final: 0.6596 (mt-10) REVERT: A 275 LYS cc_start: 0.7829 (mtmm) cc_final: 0.7265 (mttp) REVERT: A 300 ASP cc_start: 0.8088 (m-30) cc_final: 0.7847 (m-30) REVERT: A 347 LYS cc_start: 0.6751 (mttp) cc_final: 0.5792 (mtmt) REVERT: B 17 LYS cc_start: 0.7228 (tttm) cc_final: 0.6517 (ttpt) REVERT: B 208 GLU cc_start: 0.6912 (mp0) cc_final: 0.6509 (mp0) REVERT: B 253 GLU cc_start: 0.7791 (tm-30) cc_final: 0.6591 (mt-10) REVERT: B 275 LYS cc_start: 0.7819 (mtmm) cc_final: 0.7263 (mttp) REVERT: B 300 ASP cc_start: 0.8083 (m-30) cc_final: 0.7840 (m-30) REVERT: B 314 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7264 (tptt) REVERT: B 347 LYS cc_start: 0.6739 (mttp) cc_final: 0.5773 (mtmt) REVERT: C 17 LYS cc_start: 0.7189 (tttm) cc_final: 0.6485 (ttpt) REVERT: C 208 GLU cc_start: 0.6927 (mp0) cc_final: 0.6519 (mp0) REVERT: C 253 GLU cc_start: 0.7787 (tm-30) cc_final: 0.6581 (mt-10) REVERT: C 275 LYS cc_start: 0.7829 (mtmm) cc_final: 0.7279 (mttp) REVERT: C 300 ASP cc_start: 0.8077 (m-30) cc_final: 0.7833 (m-30) REVERT: C 314 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7268 (tptt) REVERT: C 347 LYS cc_start: 0.6651 (OUTLIER) cc_final: 0.5591 (mtmt) REVERT: D 17 LYS cc_start: 0.7178 (tttm) cc_final: 0.6485 (ttpt) REVERT: D 208 GLU cc_start: 0.6925 (mp0) cc_final: 0.6512 (mp0) REVERT: D 253 GLU cc_start: 0.7784 (tm-30) cc_final: 0.6582 (mt-10) REVERT: D 275 LYS cc_start: 0.7825 (mtmm) cc_final: 0.7273 (mttp) REVERT: D 300 ASP cc_start: 0.8085 (m-30) cc_final: 0.7844 (m-30) REVERT: D 347 LYS cc_start: 0.6707 (mttm) cc_final: 0.5641 (mtmt) outliers start: 26 outliers final: 23 residues processed: 166 average time/residue: 0.5725 time to fit residues: 102.5420 Evaluate side-chains 162 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 245 VAL Chi-restraints excluded: chain A residue 289 SER 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 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 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 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 C residue 347 LYS Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 33 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 119 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3363 r_free = 0.3363 target = 0.125544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.099707 restraints weight = 9843.459| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.34 r_work: 0.2895 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 10786 Z= 0.240 Angle : 0.575 8.564 14640 Z= 0.283 Chirality : 0.048 0.147 1624 Planarity : 0.004 0.030 1856 Dihedral : 9.607 58.846 1708 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.36 % Allowed : 23.60 % Favored : 73.04 % 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: -0.97 (0.22), residues: 1380 helix: 0.21 (0.24), residues: 460 sheet: -1.27 (0.31), residues: 260 loop : -0.88 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 211 TYR 0.016 0.002 TYR B 258 PHE 0.014 0.002 PHE D 221 TRP 0.009 0.002 TRP C 92 HIS 0.002 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00571 (10756) covalent geometry : angle 0.56620 (14612) SS BOND : bond 0.00251 ( 2) SS BOND : angle 0.55731 ( 4) hydrogen bonds : bond 0.03527 ( 400) hydrogen bonds : angle 5.11824 ( 1176) metal coordination : bond 0.00677 ( 28) metal coordination : angle 2.53099 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3376.68 seconds wall clock time: 58 minutes 32.73 seconds (3512.73 seconds total)