Starting phenix.real_space_refine on Mon Jul 28 17:37:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kcb_22807/07_2025/7kcb_22807.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kcb_22807/07_2025/7kcb_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_22807/07_2025/7kcb_22807.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kcb_22807/07_2025/7kcb_22807.map" model { file = "/net/cci-nas-00/data/ceres_data/7kcb_22807/07_2025/7kcb_22807.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kcb_22807/07_2025/7kcb_22807.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: C, B, D Time building chain proxies: 5.40, per 1000 atoms: 0.51 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 C 277 " - pdb=" SG CYS B 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: 2.88 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.61 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: 3.41 Time building geometry restraints manager: 3.29 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.950 Find NCS groups from input model: 0.200 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:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.450 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.002 TRP B 172 HIS 0.009 0.002 HIS B 240 PHE 0.017 0.003 PHE B 221 TYR 0.017 0.003 TYR C 258 ARG 0.003 0.001 ARG A 260 Details of bonding type rmsd hydrogen bonds : bond 0.16409 ( 400) hydrogen bonds : angle 8.51356 ( 1176) metal coordination : bond 0.12421 ( 28) metal coordination : angle 7.20305 ( 24) SS BOND : bond 0.06347 ( 2) SS BOND : angle 1.70741 ( 4) covalent geometry : bond 0.01117 (10756) covalent geometry : angle 0.90995 (14612) *********************** 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 : 1.084 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: 1.2676 time to fit residues: 240.4553 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 : 1.147 ------------------------------------------------------------------------------- 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 114 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.132473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.106817 restraints weight = 9640.195| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.34 r_work: 0.2979 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10786 Z= 0.126 Angle : 0.500 4.494 14640 Z= 0.256 Chirality : 0.045 0.137 1624 Planarity : 0.004 0.045 1856 Dihedral : 9.317 57.846 1736 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.50 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.20), residues: 1380 helix: -0.50 (0.24), residues: 452 sheet: -1.41 (0.29), residues: 240 loop : -1.51 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 50 HIS 0.002 0.001 HIS D 48 PHE 0.012 0.002 PHE B 221 TYR 0.016 0.001 TYR B 258 ARG 0.002 0.000 ARG D 310 Details of bonding type rmsd hydrogen bonds : bond 0.03352 ( 400) hydrogen bonds : angle 5.57356 ( 1176) metal coordination : bond 0.00256 ( 28) metal coordination : angle 2.01719 ( 24) SS BOND : bond 0.00899 ( 2) SS BOND : angle 0.74375 ( 4) covalent geometry : bond 0.00283 (10756) covalent geometry : angle 0.49402 (14612) *********************** 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 : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.7995 (t) REVERT: A 17 LYS cc_start: 0.6513 (tttm) cc_final: 0.5825 (ttpt) REVERT: A 208 GLU cc_start: 0.7032 (mp0) cc_final: 0.6776 (mp0) REVERT: A 275 LYS cc_start: 0.7920 (mtmm) cc_final: 0.7436 (mttp) REVERT: A 300 ASP cc_start: 0.8157 (m-30) cc_final: 0.7879 (m-30) REVERT: B 5 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.8011 (t) REVERT: B 17 LYS cc_start: 0.6499 (tttm) cc_final: 0.5809 (ttpt) REVERT: B 208 GLU cc_start: 0.7026 (mp0) cc_final: 0.6769 (mp0) REVERT: B 275 LYS cc_start: 0.7933 (mtmm) cc_final: 0.7422 (mttp) REVERT: B 300 ASP cc_start: 0.8133 (m-30) cc_final: 0.7848 (m-30) REVERT: C 5 THR cc_start: 0.8340 (OUTLIER) cc_final: 0.8009 (t) REVERT: C 17 LYS cc_start: 0.6518 (tttm) cc_final: 0.5821 (ttpt) REVERT: C 208 GLU cc_start: 0.7037 (mp0) cc_final: 0.6782 (mp0) REVERT: C 275 LYS cc_start: 0.7929 (mtmm) cc_final: 0.7427 (mttp) REVERT: C 300 ASP cc_start: 0.8135 (m-30) cc_final: 0.7855 (m-30) REVERT: D 5 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.7997 (t) REVERT: D 17 LYS cc_start: 0.6534 (tttm) cc_final: 0.5836 (ttpt) REVERT: D 208 GLU cc_start: 0.7052 (mp0) cc_final: 0.6796 (mp0) REVERT: D 275 LYS cc_start: 0.7928 (mtmm) cc_final: 0.7450 (mttp) REVERT: D 300 ASP cc_start: 0.8149 (m-30) cc_final: 0.7874 (m-30) outliers start: 24 outliers final: 8 residues processed: 152 average time/residue: 1.6192 time to fit residues: 264.8244 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 : 1.114 ------------------------------------------------------------------------------- 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 63 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 39 optimal weight: 0.0170 chunk 78 optimal weight: 0.9990 chunk 2 optimal weight: 0.0570 chunk 56 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.134046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.108211 restraints weight = 9685.142| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.35 r_work: 0.2999 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10786 Z= 0.105 Angle : 0.463 6.163 14640 Z= 0.235 Chirality : 0.044 0.136 1624 Planarity : 0.004 0.038 1856 Dihedral : 8.850 58.327 1708 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.61 % Allowed : 23.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.21), residues: 1380 helix: 0.14 (0.25), residues: 456 sheet: -1.27 (0.31), residues: 240 loop : -1.09 (0.21), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 54 HIS 0.003 0.001 HIS C 48 PHE 0.008 0.001 PHE C 221 TYR 0.015 0.001 TYR B 258 ARG 0.002 0.000 ARG C 310 Details of bonding type rmsd hydrogen bonds : bond 0.03097 ( 400) hydrogen bonds : angle 5.07108 ( 1176) metal coordination : bond 0.00159 ( 28) metal coordination : angle 1.55995 ( 24) SS BOND : bond 0.00201 ( 2) SS BOND : angle 1.01022 ( 4) covalent geometry : bond 0.00238 (10756) covalent geometry : angle 0.45891 (14612) *********************** 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 154 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 1.148 Fit side-chains REVERT: A 5 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.7960 (t) REVERT: A 17 LYS cc_start: 0.6519 (tttm) cc_final: 0.5825 (ttpt) REVERT: A 168 MET cc_start: 0.8891 (mtm) cc_final: 0.8636 (mtp) REVERT: A 208 GLU cc_start: 0.7048 (mp0) cc_final: 0.6711 (mp0) REVERT: A 275 LYS cc_start: 0.8006 (mtmm) cc_final: 0.7469 (mttp) REVERT: A 300 ASP cc_start: 0.8120 (m-30) cc_final: 0.7862 (m-30) REVERT: A 347 LYS cc_start: 0.6291 (mttm) cc_final: 0.5621 (mtmt) REVERT: B 5 THR cc_start: 0.8292 (OUTLIER) cc_final: 0.7964 (t) REVERT: B 17 LYS cc_start: 0.6509 (tttm) cc_final: 0.5808 (ttpt) REVERT: B 168 MET cc_start: 0.8897 (mtm) cc_final: 0.8638 (mtp) REVERT: B 208 GLU cc_start: 0.7061 (mp0) cc_final: 0.6725 (mp0) REVERT: B 275 LYS cc_start: 0.8010 (mtmm) cc_final: 0.7473 (mttp) REVERT: B 300 ASP cc_start: 0.8113 (m-30) cc_final: 0.7835 (m-30) REVERT: B 347 LYS cc_start: 0.6266 (mttm) cc_final: 0.5584 (mtmt) REVERT: C 5 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.7972 (t) REVERT: C 17 LYS cc_start: 0.6526 (tttm) cc_final: 0.5824 (ttpt) REVERT: C 168 MET cc_start: 0.8873 (mtm) cc_final: 0.8613 (mtp) REVERT: C 208 GLU cc_start: 0.7055 (mp0) cc_final: 0.6714 (mp0) REVERT: C 275 LYS cc_start: 0.7980 (mtmm) cc_final: 0.7427 (mttp) REVERT: C 277 CYS cc_start: 0.7819 (m) cc_final: 0.7585 (m) REVERT: C 300 ASP cc_start: 0.8113 (m-30) cc_final: 0.7850 (m-30) REVERT: C 347 LYS cc_start: 0.6313 (mttm) cc_final: 0.5642 (mtmt) REVERT: D 5 THR cc_start: 0.8293 (OUTLIER) cc_final: 0.7965 (t) REVERT: D 17 LYS cc_start: 0.6544 (tttm) cc_final: 0.5849 (ttpt) REVERT: D 168 MET cc_start: 0.8878 (mtm) cc_final: 0.8619 (mtp) REVERT: D 208 GLU cc_start: 0.7066 (mp0) cc_final: 0.6724 (mp0) REVERT: D 275 LYS cc_start: 0.7992 (mtmm) cc_final: 0.7446 (mttp) REVERT: D 277 CYS cc_start: 0.7804 (m) cc_final: 0.7565 (m) REVERT: D 300 ASP cc_start: 0.8103 (m-30) cc_final: 0.7832 (m-30) REVERT: D 347 LYS cc_start: 0.6316 (mttm) cc_final: 0.5638 (mtmt) outliers start: 28 outliers final: 13 residues processed: 150 average time/residue: 1.3768 time to fit residues: 222.2745 Evaluate side-chains 130 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 245 VAL Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 294 TYR 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 245 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 41 optimal weight: 0.4980 chunk 57 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 123 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS A 147 GLN B 113 HIS B 147 GLN C 113 HIS C 147 GLN D 113 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 = 0.3412 r_free = 0.3412 target = 0.130407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.104391 restraints weight = 9661.392| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.34 r_work: 0.2961 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: 0.7726 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10786 Z= 0.140 Angle : 0.479 5.214 14640 Z= 0.243 Chirality : 0.045 0.137 1624 Planarity : 0.003 0.031 1856 Dihedral : 9.107 59.044 1708 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.10 % Allowed : 22.01 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.21), residues: 1380 helix: 0.24 (0.25), residues: 456 sheet: -1.16 (0.32), residues: 236 loop : -1.03 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 92 HIS 0.002 0.000 HIS B 48 PHE 0.012 0.001 PHE C 221 TYR 0.015 0.001 TYR B 258 ARG 0.002 0.000 ARG B 340 Details of bonding type rmsd hydrogen bonds : bond 0.03230 ( 400) hydrogen bonds : angle 4.96183 ( 1176) metal coordination : bond 0.00268 ( 28) metal coordination : angle 1.63887 ( 24) SS BOND : bond 0.00074 ( 2) SS BOND : angle 0.73108 ( 4) covalent geometry : bond 0.00328 (10756) covalent geometry : angle 0.47421 (14612) *********************** 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 170 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 126 time to evaluate : 1.132 Fit side-chains REVERT: A 5 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7904 (t) REVERT: A 17 LYS cc_start: 0.6769 (tttm) cc_final: 0.6150 (ttpt) REVERT: A 77 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7334 (mt-10) REVERT: A 182 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8414 (mp) REVERT: A 208 GLU cc_start: 0.6962 (mp0) cc_final: 0.6728 (mp0) REVERT: A 275 LYS cc_start: 0.7969 (mtmm) cc_final: 0.7478 (mttp) REVERT: A 300 ASP cc_start: 0.8121 (m-30) cc_final: 0.7838 (m-30) REVERT: A 347 LYS cc_start: 0.6530 (mttm) cc_final: 0.5758 (mtmt) REVERT: B 5 THR cc_start: 0.8220 (OUTLIER) cc_final: 0.7918 (t) REVERT: B 17 LYS cc_start: 0.6772 (tttm) cc_final: 0.6140 (ttpt) REVERT: B 77 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7322 (mt-10) REVERT: B 182 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8415 (mp) REVERT: B 208 GLU cc_start: 0.6960 (mp0) cc_final: 0.6723 (mp0) REVERT: B 275 LYS cc_start: 0.7961 (mtmm) cc_final: 0.7469 (mttp) REVERT: B 300 ASP cc_start: 0.8122 (m-30) cc_final: 0.7838 (m-30) REVERT: B 347 LYS cc_start: 0.6524 (mttm) cc_final: 0.5754 (mtmt) REVERT: C 5 THR cc_start: 0.8220 (OUTLIER) cc_final: 0.7922 (t) REVERT: C 17 LYS cc_start: 0.6771 (tttm) cc_final: 0.6143 (ttpt) REVERT: C 77 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7309 (mt-10) REVERT: C 182 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8417 (mp) REVERT: C 208 GLU cc_start: 0.6973 (mp0) cc_final: 0.6735 (mp0) REVERT: C 275 LYS cc_start: 0.7968 (mtmm) cc_final: 0.7466 (mttp) REVERT: C 277 CYS cc_start: 0.7810 (m) cc_final: 0.7583 (m) REVERT: C 300 ASP cc_start: 0.8114 (m-30) cc_final: 0.7828 (m-30) REVERT: C 347 LYS cc_start: 0.6541 (mttm) cc_final: 0.5767 (mtmt) REVERT: D 5 THR cc_start: 0.8211 (OUTLIER) cc_final: 0.7914 (t) REVERT: D 17 LYS cc_start: 0.6782 (tttm) cc_final: 0.6157 (ttpt) REVERT: D 77 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7306 (mt-10) REVERT: D 182 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8411 (mp) REVERT: D 208 GLU cc_start: 0.6974 (mp0) cc_final: 0.6733 (mp0) REVERT: D 275 LYS cc_start: 0.7976 (mtmm) cc_final: 0.7480 (mttp) REVERT: D 277 CYS cc_start: 0.7778 (m) cc_final: 0.7543 (m) REVERT: D 300 ASP cc_start: 0.8109 (m-30) cc_final: 0.7821 (m-30) REVERT: D 347 LYS cc_start: 0.6514 (mttm) cc_final: 0.5747 (mtmt) outliers start: 44 outliers final: 20 residues processed: 162 average time/residue: 1.4194 time to fit residues: 250.0831 Evaluate side-chains 155 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 77 GLU 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 5 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 77 GLU 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 5 THR Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 77 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 54 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 115 optimal weight: 10.0000 chunk 59 optimal weight: 0.5980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS A 147 GLN B 113 HIS B 147 GLN C 113 HIS C 147 GLN D 113 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 = 0.3384 r_free = 0.3384 target = 0.127890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.101956 restraints weight = 9757.978| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.34 r_work: 0.2940 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10786 Z= 0.178 Angle : 0.505 5.492 14640 Z= 0.255 Chirality : 0.046 0.137 1624 Planarity : 0.003 0.027 1856 Dihedral : 9.342 58.003 1708 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.20 % Allowed : 21.92 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.21), residues: 1380 helix: 0.10 (0.24), residues: 464 sheet: -1.21 (0.32), residues: 236 loop : -1.03 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 92 HIS 0.002 0.000 HIS B 240 PHE 0.013 0.002 PHE A 221 TYR 0.015 0.001 TYR C 258 ARG 0.003 0.000 ARG D 310 Details of bonding type rmsd hydrogen bonds : bond 0.03347 ( 400) hydrogen bonds : angle 5.02418 ( 1176) metal coordination : bond 0.00380 ( 28) metal coordination : angle 1.80801 ( 24) SS BOND : bond 0.00143 ( 2) SS BOND : angle 0.60277 ( 4) covalent geometry : bond 0.00422 (10756) covalent geometry : angle 0.50053 (14612) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 136 time to evaluate : 1.043 Fit side-chains REVERT: A 5 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.8000 (t) REVERT: A 17 LYS cc_start: 0.6949 (tttm) cc_final: 0.6212 (ttpt) REVERT: A 182 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8424 (mp) REVERT: A 208 GLU cc_start: 0.6841 (mp0) cc_final: 0.6569 (mp0) REVERT: A 275 LYS cc_start: 0.7945 (mtmm) cc_final: 0.7426 (mttp) REVERT: A 300 ASP cc_start: 0.8139 (m-30) cc_final: 0.7853 (m-30) REVERT: A 347 LYS cc_start: 0.6694 (mttm) cc_final: 0.5890 (mtmt) REVERT: B 5 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.8007 (t) REVERT: B 17 LYS cc_start: 0.6896 (tttm) cc_final: 0.6197 (ttpt) REVERT: B 182 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8419 (mp) REVERT: B 208 GLU cc_start: 0.6853 (mp0) cc_final: 0.6581 (mp0) REVERT: B 275 LYS cc_start: 0.7930 (mtmm) cc_final: 0.7417 (mttp) REVERT: B 300 ASP cc_start: 0.8134 (m-30) cc_final: 0.7846 (m-30) REVERT: B 347 LYS cc_start: 0.6686 (mttm) cc_final: 0.5895 (mtmt) REVERT: C 5 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.8013 (t) REVERT: C 17 LYS cc_start: 0.6942 (tttm) cc_final: 0.6229 (ttpt) REVERT: C 182 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8418 (mp) REVERT: C 208 GLU cc_start: 0.6850 (mp0) cc_final: 0.6580 (mp0) REVERT: C 275 LYS cc_start: 0.7927 (mtmm) cc_final: 0.7423 (mttp) REVERT: C 300 ASP cc_start: 0.8132 (m-30) cc_final: 0.7844 (m-30) REVERT: C 347 LYS cc_start: 0.6709 (mttm) cc_final: 0.5903 (mtmt) REVERT: D 5 THR cc_start: 0.8257 (OUTLIER) cc_final: 0.8017 (t) REVERT: D 17 LYS cc_start: 0.6966 (tttm) cc_final: 0.6224 (ttpt) REVERT: D 182 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8421 (mp) REVERT: D 208 GLU cc_start: 0.6858 (mp0) cc_final: 0.6583 (mp0) REVERT: D 275 LYS cc_start: 0.7931 (mtmm) cc_final: 0.7436 (mttp) REVERT: D 300 ASP cc_start: 0.8119 (m-30) cc_final: 0.7832 (m-30) REVERT: D 347 LYS cc_start: 0.6680 (mttm) cc_final: 0.5873 (mtmt) outliers start: 45 outliers final: 24 residues processed: 173 average time/residue: 1.1715 time to fit residues: 218.9616 Evaluate side-chains 159 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 313 VAL 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 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 C residue 313 VAL 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 Chi-restraints excluded: chain D residue 313 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 52 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3402 r_free = 0.3402 target = 0.129514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.103532 restraints weight = 9740.038| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.34 r_work: 0.2955 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10786 Z= 0.136 Angle : 0.479 5.278 14640 Z= 0.242 Chirality : 0.045 0.137 1624 Planarity : 0.003 0.028 1856 Dihedral : 9.175 56.840 1708 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.99 % Allowed : 23.69 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.21), residues: 1380 helix: 0.30 (0.24), residues: 464 sheet: -1.22 (0.32), residues: 236 loop : -0.90 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 92 HIS 0.001 0.000 HIS B 240 PHE 0.012 0.001 PHE B 221 TYR 0.015 0.001 TYR C 258 ARG 0.002 0.000 ARG A 260 Details of bonding type rmsd hydrogen bonds : bond 0.03102 ( 400) hydrogen bonds : angle 4.89847 ( 1176) metal coordination : bond 0.00249 ( 28) metal coordination : angle 1.72169 ( 24) SS BOND : bond 0.00114 ( 2) SS BOND : angle 0.47645 ( 4) covalent geometry : bond 0.00317 (10756) covalent geometry : angle 0.47384 (14612) *********************** 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 170 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 1.365 Fit side-chains REVERT: A 5 THR cc_start: 0.8278 (OUTLIER) cc_final: 0.8053 (t) REVERT: A 17 LYS cc_start: 0.6897 (tttm) cc_final: 0.6196 (ttpt) REVERT: A 182 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8402 (mp) REVERT: A 208 GLU cc_start: 0.6949 (mp0) cc_final: 0.6646 (mp0) REVERT: A 253 GLU cc_start: 0.7779 (tm-30) cc_final: 0.6613 (mt-10) REVERT: A 275 LYS cc_start: 0.7871 (mtmm) cc_final: 0.7280 (mttp) REVERT: A 300 ASP cc_start: 0.8040 (m-30) cc_final: 0.7785 (m-30) REVERT: A 347 LYS cc_start: 0.6694 (mttm) cc_final: 0.5803 (mtmt) REVERT: B 5 THR cc_start: 0.8281 (OUTLIER) cc_final: 0.8049 (t) REVERT: B 17 LYS cc_start: 0.6943 (tttm) cc_final: 0.6223 (ttpt) REVERT: B 182 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8395 (mp) REVERT: B 208 GLU cc_start: 0.6961 (mp0) cc_final: 0.6656 (mp0) REVERT: B 253 GLU cc_start: 0.7761 (tm-30) cc_final: 0.6594 (mt-10) REVERT: B 275 LYS cc_start: 0.7855 (mtmm) cc_final: 0.7271 (mttp) REVERT: B 300 ASP cc_start: 0.8042 (m-30) cc_final: 0.7788 (m-30) REVERT: B 347 LYS cc_start: 0.6689 (mttm) cc_final: 0.5806 (mtmt) REVERT: C 5 THR cc_start: 0.8274 (OUTLIER) cc_final: 0.8049 (t) REVERT: C 17 LYS cc_start: 0.6935 (tttm) cc_final: 0.6277 (ttpt) REVERT: C 182 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8396 (mp) REVERT: C 208 GLU cc_start: 0.6835 (mp0) cc_final: 0.6534 (mp0) REVERT: C 275 LYS cc_start: 0.7785 (mtmm) cc_final: 0.7351 (mttp) REVERT: C 300 ASP cc_start: 0.8030 (m-30) cc_final: 0.7776 (m-30) REVERT: C 347 LYS cc_start: 0.6689 (mttm) cc_final: 0.5799 (mtmt) REVERT: D 5 THR cc_start: 0.8280 (OUTLIER) cc_final: 0.8058 (t) REVERT: D 17 LYS cc_start: 0.6956 (tttm) cc_final: 0.6296 (ttpt) REVERT: D 182 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8401 (mp) REVERT: D 208 GLU cc_start: 0.6970 (mp0) cc_final: 0.6664 (mp0) REVERT: D 253 GLU cc_start: 0.7752 (tm-30) cc_final: 0.6593 (mt-10) REVERT: D 275 LYS cc_start: 0.7801 (mtmm) cc_final: 0.7307 (mttp) REVERT: D 300 ASP cc_start: 0.8029 (m-30) cc_final: 0.7774 (m-30) REVERT: D 347 LYS cc_start: 0.6672 (mttm) cc_final: 0.5967 (mtmt) outliers start: 32 outliers final: 19 residues processed: 162 average time/residue: 1.6988 time to fit residues: 297.0743 Evaluate side-chains 162 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 5.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 D residue 5 THR 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 102 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.131928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.106023 restraints weight = 9789.891| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.36 r_work: 0.2974 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10786 Z= 0.128 Angle : 0.473 5.456 14640 Z= 0.238 Chirality : 0.044 0.135 1624 Planarity : 0.003 0.027 1856 Dihedral : 9.116 56.978 1708 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.94 % Allowed : 22.67 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.21), residues: 1380 helix: 0.46 (0.24), residues: 460 sheet: -1.25 (0.32), residues: 236 loop : -0.79 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 92 HIS 0.001 0.000 HIS B 121 PHE 0.011 0.001 PHE A 221 TYR 0.014 0.001 TYR A 258 ARG 0.003 0.000 ARG B 310 Details of bonding type rmsd hydrogen bonds : bond 0.03011 ( 400) hydrogen bonds : angle 4.82956 ( 1176) metal coordination : bond 0.00220 ( 28) metal coordination : angle 1.70896 ( 24) SS BOND : bond 0.00121 ( 2) SS BOND : angle 0.43022 ( 4) covalent geometry : bond 0.00298 (10756) covalent geometry : angle 0.46861 (14612) *********************** 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 188 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 135 time to evaluate : 1.060 Fit side-chains REVERT: A 5 THR cc_start: 0.8250 (OUTLIER) cc_final: 0.8037 (t) REVERT: A 17 LYS cc_start: 0.6952 (tttm) cc_final: 0.6299 (ttpt) REVERT: A 208 GLU cc_start: 0.6798 (mp0) cc_final: 0.6534 (mp0) REVERT: A 253 GLU cc_start: 0.7785 (tm-30) cc_final: 0.6608 (mt-10) REVERT: A 275 LYS cc_start: 0.7823 (mtmm) cc_final: 0.7280 (mttp) REVERT: A 300 ASP cc_start: 0.8093 (m-30) cc_final: 0.7828 (m-30) REVERT: A 347 LYS cc_start: 0.6647 (mttm) cc_final: 0.5733 (mtmt) REVERT: B 5 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.8030 (t) REVERT: B 17 LYS cc_start: 0.6952 (tttm) cc_final: 0.6221 (ttpt) REVERT: B 208 GLU cc_start: 0.6814 (mp0) cc_final: 0.6556 (mp0) REVERT: B 253 GLU cc_start: 0.7771 (tm-30) cc_final: 0.6593 (mt-10) REVERT: B 275 LYS cc_start: 0.7805 (mtmm) cc_final: 0.7268 (mttp) REVERT: B 300 ASP cc_start: 0.8082 (m-30) cc_final: 0.7817 (m-30) REVERT: B 347 LYS cc_start: 0.6688 (OUTLIER) cc_final: 0.5786 (mtmt) REVERT: C 5 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.8042 (t) REVERT: C 17 LYS cc_start: 0.6948 (tttm) cc_final: 0.6288 (ttpt) REVERT: C 208 GLU cc_start: 0.6786 (mp0) cc_final: 0.6528 (mp0) REVERT: C 253 GLU cc_start: 0.7771 (tm-30) cc_final: 0.6591 (mt-10) REVERT: C 275 LYS cc_start: 0.7797 (mtmm) cc_final: 0.7269 (mttp) REVERT: C 300 ASP cc_start: 0.8086 (m-30) cc_final: 0.7817 (m-30) REVERT: C 347 LYS cc_start: 0.6654 (mttm) cc_final: 0.5724 (mtmt) REVERT: D 5 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.8050 (t) REVERT: D 17 LYS cc_start: 0.6960 (tttm) cc_final: 0.6301 (ttpt) REVERT: D 208 GLU cc_start: 0.6814 (mp0) cc_final: 0.6550 (mp0) REVERT: D 253 GLU cc_start: 0.7766 (tm-30) cc_final: 0.6585 (mt-10) REVERT: D 275 LYS cc_start: 0.7820 (mtmm) cc_final: 0.7298 (mttp) REVERT: D 300 ASP cc_start: 0.8036 (m-30) cc_final: 0.7780 (m-30) REVERT: D 347 LYS cc_start: 0.6639 (mttm) cc_final: 0.5688 (mtmt) outliers start: 53 outliers final: 32 residues processed: 179 average time/residue: 1.8017 time to fit residues: 348.4276 Evaluate side-chains 172 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 337 ILE 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 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 337 ILE Chi-restraints excluded: chain B residue 347 LYS 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 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 337 ILE 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 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 337 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 132 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 127 optimal weight: 0.4980 chunk 94 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.126053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.100079 restraints weight = 9773.960| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.34 r_work: 0.2931 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 10786 Z= 0.233 Angle : 0.562 6.684 14640 Z= 0.281 Chirality : 0.047 0.144 1624 Planarity : 0.004 0.026 1856 Dihedral : 9.563 57.477 1708 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.36 % Allowed : 24.25 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.22), residues: 1380 helix: 0.25 (0.24), residues: 460 sheet: -1.24 (0.31), residues: 260 loop : -0.81 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 92 HIS 0.002 0.001 HIS A 48 PHE 0.015 0.002 PHE A 221 TYR 0.017 0.002 TYR A 258 ARG 0.001 0.000 ARG A 340 Details of bonding type rmsd hydrogen bonds : bond 0.03517 ( 400) hydrogen bonds : angle 5.07525 ( 1176) metal coordination : bond 0.00613 ( 28) metal coordination : angle 2.26759 ( 24) SS BOND : bond 0.00213 ( 2) SS BOND : angle 0.57729 ( 4) covalent geometry : bond 0.00556 (10756) covalent geometry : angle 0.55524 (14612) *********************** 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 178 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 1.464 Fit side-chains REVERT: A 17 LYS cc_start: 0.7245 (tttm) cc_final: 0.6557 (ttpt) REVERT: A 182 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8205 (mp) REVERT: A 208 GLU cc_start: 0.6843 (mp0) cc_final: 0.6503 (mp0) REVERT: A 253 GLU cc_start: 0.7874 (tm-30) cc_final: 0.6787 (mt-10) REVERT: A 275 LYS cc_start: 0.7891 (mtmm) cc_final: 0.7288 (mttp) REVERT: A 300 ASP cc_start: 0.8129 (m-30) cc_final: 0.7861 (m-30) REVERT: A 347 LYS cc_start: 0.6653 (mttm) cc_final: 0.5706 (mtmt) REVERT: B 17 LYS cc_start: 0.7236 (tttm) cc_final: 0.6554 (ttpt) REVERT: B 182 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8202 (mp) REVERT: B 208 GLU cc_start: 0.6852 (mp0) cc_final: 0.6512 (mp0) REVERT: B 253 GLU cc_start: 0.7858 (tm-30) cc_final: 0.6783 (mt-10) REVERT: B 275 LYS cc_start: 0.7883 (mtmm) cc_final: 0.7281 (mttp) REVERT: B 300 ASP cc_start: 0.8121 (m-30) cc_final: 0.7854 (m-30) REVERT: B 347 LYS cc_start: 0.6640 (OUTLIER) cc_final: 0.5722 (mtmt) REVERT: C 17 LYS cc_start: 0.7243 (tttm) cc_final: 0.6546 (ttpt) REVERT: C 182 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8205 (mp) REVERT: C 208 GLU cc_start: 0.6864 (mp0) cc_final: 0.6526 (mp0) REVERT: C 253 GLU cc_start: 0.7859 (tm-30) cc_final: 0.6778 (mt-10) REVERT: C 275 LYS cc_start: 0.7900 (mtmm) cc_final: 0.7264 (mttp) REVERT: C 300 ASP cc_start: 0.8121 (m-30) cc_final: 0.7851 (m-30) REVERT: C 347 LYS cc_start: 0.6642 (mttm) cc_final: 0.5697 (mtmt) REVERT: D 17 LYS cc_start: 0.7255 (tttm) cc_final: 0.6563 (ttpt) REVERT: D 182 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8202 (mp) REVERT: D 208 GLU cc_start: 0.6867 (mp0) cc_final: 0.6523 (mp0) REVERT: D 253 GLU cc_start: 0.7848 (tm-30) cc_final: 0.6784 (mt-10) REVERT: D 275 LYS cc_start: 0.7914 (mtmm) cc_final: 0.7290 (mttp) REVERT: D 300 ASP cc_start: 0.8066 (m-30) cc_final: 0.7792 (m-30) REVERT: D 347 LYS cc_start: 0.6668 (mttm) cc_final: 0.5717 (mtmt) outliers start: 36 outliers final: 28 residues processed: 173 average time/residue: 1.2488 time to fit residues: 232.5369 Evaluate side-chains 172 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 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 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 54 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 115 optimal weight: 8.9990 chunk 114 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 133 optimal weight: 0.0670 chunk 118 optimal weight: 2.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- 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 = 0.3406 r_free = 0.3406 target = 0.129563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.103721 restraints weight = 9763.250| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.35 r_work: 0.2962 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10786 Z= 0.132 Angle : 0.496 7.705 14640 Z= 0.247 Chirality : 0.044 0.136 1624 Planarity : 0.003 0.028 1856 Dihedral : 9.203 57.819 1708 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.08 % Allowed : 24.53 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.22), residues: 1380 helix: 0.53 (0.25), residues: 460 sheet: -1.23 (0.32), residues: 236 loop : -0.75 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 54 HIS 0.001 0.000 HIS D 138 PHE 0.012 0.001 PHE C 221 TYR 0.015 0.001 TYR A 258 ARG 0.002 0.000 ARG B 260 Details of bonding type rmsd hydrogen bonds : bond 0.03012 ( 400) hydrogen bonds : angle 4.85576 ( 1176) metal coordination : bond 0.00229 ( 28) metal coordination : angle 1.89235 ( 24) SS BOND : bond 0.00129 ( 2) SS BOND : angle 0.44348 ( 4) covalent geometry : bond 0.00310 (10756) covalent geometry : angle 0.49014 (14612) *********************** 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 165 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 1.132 Fit side-chains REVERT: A 17 LYS cc_start: 0.7280 (tttm) cc_final: 0.6584 (ttpt) REVERT: A 208 GLU cc_start: 0.6871 (mp0) cc_final: 0.6594 (mp0) REVERT: A 253 GLU cc_start: 0.7781 (tm-30) cc_final: 0.6607 (mt-10) REVERT: A 275 LYS cc_start: 0.7823 (mtmm) cc_final: 0.7265 (mttp) REVERT: A 300 ASP cc_start: 0.8080 (m-30) cc_final: 0.7841 (m-30) REVERT: A 347 LYS cc_start: 0.6652 (mttm) cc_final: 0.5623 (mtmt) REVERT: B 17 LYS cc_start: 0.7264 (tttm) cc_final: 0.6586 (ttpt) REVERT: B 208 GLU cc_start: 0.6851 (mp0) cc_final: 0.6575 (mp0) REVERT: B 253 GLU cc_start: 0.7760 (tm-30) cc_final: 0.6596 (mt-10) REVERT: B 275 LYS cc_start: 0.7797 (mtmm) cc_final: 0.7242 (mttp) REVERT: B 300 ASP cc_start: 0.8074 (m-30) cc_final: 0.7834 (m-30) REVERT: B 347 LYS cc_start: 0.6648 (OUTLIER) cc_final: 0.5655 (mtmt) REVERT: C 17 LYS cc_start: 0.7272 (tttm) cc_final: 0.6569 (ttpt) REVERT: C 208 GLU cc_start: 0.6884 (mp0) cc_final: 0.6610 (mp0) REVERT: C 253 GLU cc_start: 0.7766 (tm-30) cc_final: 0.6589 (mt-10) REVERT: C 275 LYS cc_start: 0.7728 (mtmm) cc_final: 0.7248 (mttp) REVERT: C 300 ASP cc_start: 0.8071 (m-30) cc_final: 0.7827 (m-30) REVERT: C 347 LYS cc_start: 0.6658 (mttm) cc_final: 0.5624 (mtmt) REVERT: D 17 LYS cc_start: 0.7267 (tttm) cc_final: 0.6584 (ttpt) REVERT: D 208 GLU cc_start: 0.6857 (mp0) cc_final: 0.6576 (mp0) REVERT: D 253 GLU cc_start: 0.7755 (tm-30) cc_final: 0.6588 (mt-10) REVERT: D 275 LYS cc_start: 0.7756 (mtmm) cc_final: 0.7276 (mttp) REVERT: D 300 ASP cc_start: 0.8044 (m-30) cc_final: 0.7801 (m-30) REVERT: D 347 LYS cc_start: 0.6671 (mttm) cc_final: 0.5632 (mtmt) outliers start: 33 outliers final: 28 residues processed: 160 average time/residue: 1.1901 time to fit residues: 206.0338 Evaluate side-chains 159 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain 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 58 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 313 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 48 optimal weight: 0.0980 chunk 8 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.130723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.104893 restraints weight = 9673.585| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.36 r_work: 0.2961 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10786 Z= 0.140 Angle : 0.498 8.256 14640 Z= 0.248 Chirality : 0.045 0.135 1624 Planarity : 0.003 0.029 1856 Dihedral : 9.217 59.410 1708 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.71 % Allowed : 24.91 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.22), residues: 1380 helix: 0.56 (0.24), residues: 460 sheet: -1.25 (0.33), residues: 236 loop : -0.70 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 54 HIS 0.001 0.000 HIS B 121 PHE 0.012 0.001 PHE D 221 TYR 0.015 0.001 TYR D 258 ARG 0.002 0.000 ARG B 260 Details of bonding type rmsd hydrogen bonds : bond 0.03007 ( 400) hydrogen bonds : angle 4.84617 ( 1176) metal coordination : bond 0.00261 ( 28) metal coordination : angle 1.76180 ( 24) SS BOND : bond 0.00131 ( 2) SS BOND : angle 0.44920 ( 4) covalent geometry : bond 0.00327 (10756) covalent geometry : angle 0.49368 (14612) ********************** 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 159 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 1.231 Fit side-chains REVERT: A 17 LYS cc_start: 0.7296 (tttm) cc_final: 0.6596 (ttpt) REVERT: A 208 GLU cc_start: 0.6838 (mp0) cc_final: 0.6480 (mp0) REVERT: A 253 GLU cc_start: 0.7775 (tm-30) cc_final: 0.6606 (mt-10) REVERT: A 275 LYS cc_start: 0.7752 (mtmm) cc_final: 0.7226 (mttp) REVERT: A 300 ASP cc_start: 0.8048 (m-30) cc_final: 0.7798 (m-30) REVERT: A 347 LYS cc_start: 0.6682 (mttm) cc_final: 0.5637 (mtmt) REVERT: B 17 LYS cc_start: 0.7331 (tttm) cc_final: 0.6632 (ttpt) REVERT: B 208 GLU cc_start: 0.6855 (mp0) cc_final: 0.6501 (mp0) REVERT: B 253 GLU cc_start: 0.7762 (tm-30) cc_final: 0.6597 (mt-10) REVERT: B 275 LYS cc_start: 0.7733 (mtmm) cc_final: 0.7209 (mttp) REVERT: B 300 ASP cc_start: 0.8042 (m-30) cc_final: 0.7793 (m-30) REVERT: B 347 LYS cc_start: 0.6645 (OUTLIER) cc_final: 0.5583 (mtmt) REVERT: C 17 LYS cc_start: 0.7291 (tttm) cc_final: 0.6581 (ttpt) REVERT: C 208 GLU cc_start: 0.6848 (mp0) cc_final: 0.6493 (mp0) REVERT: C 253 GLU cc_start: 0.7771 (tm-30) cc_final: 0.6600 (mt-10) REVERT: C 275 LYS cc_start: 0.7744 (mtmm) cc_final: 0.7244 (mttp) REVERT: C 300 ASP cc_start: 0.8041 (m-30) cc_final: 0.7792 (m-30) REVERT: C 347 LYS cc_start: 0.6654 (mttm) cc_final: 0.5605 (mtmt) REVERT: D 17 LYS cc_start: 0.7311 (tttm) cc_final: 0.6605 (ttpt) REVERT: D 208 GLU cc_start: 0.6865 (mp0) cc_final: 0.6505 (mp0) REVERT: D 253 GLU cc_start: 0.7760 (tm-30) cc_final: 0.6591 (mt-10) REVERT: D 275 LYS cc_start: 0.7761 (mtmm) cc_final: 0.7256 (mttp) REVERT: D 300 ASP cc_start: 0.8053 (m-30) cc_final: 0.7806 (m-30) REVERT: D 347 LYS cc_start: 0.6685 (mttm) cc_final: 0.5631 (mtmt) outliers start: 29 outliers final: 28 residues processed: 154 average time/residue: 1.1596 time to fit residues: 193.1763 Evaluate side-chains 157 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain 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 58 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 313 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 8.9990 chunk 83 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 chunk 79 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3456 r_free = 0.3456 target = 0.133440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.107764 restraints weight = 9557.711| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.35 r_work: 0.2994 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10786 Z= 0.110 Angle : 0.476 8.358 14640 Z= 0.236 Chirality : 0.044 0.135 1624 Planarity : 0.003 0.028 1856 Dihedral : 8.955 59.461 1708 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.89 % Allowed : 24.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.22), residues: 1380 helix: 0.73 (0.25), residues: 460 sheet: -1.26 (0.32), residues: 236 loop : -0.67 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 54 HIS 0.002 0.000 HIS D 138 PHE 0.010 0.001 PHE C 221 TYR 0.014 0.001 TYR C 258 ARG 0.002 0.000 ARG D 260 Details of bonding type rmsd hydrogen bonds : bond 0.02810 ( 400) hydrogen bonds : angle 4.73268 ( 1176) metal coordination : bond 0.00159 ( 28) metal coordination : angle 1.69449 ( 24) SS BOND : bond 0.00104 ( 2) SS BOND : angle 0.38852 ( 4) covalent geometry : bond 0.00253 (10756) covalent geometry : angle 0.47143 (14612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7616.23 seconds wall clock time: 140 minutes 11.74 seconds (8411.74 seconds total)