Starting phenix.real_space_refine on Wed Mar 4 11:54:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n28_9326/03_2026/6n28_9326_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n28_9326/03_2026/6n28_9326.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6n28_9326/03_2026/6n28_9326.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n28_9326/03_2026/6n28_9326.map" model { file = "/net/cci-nas-00/data/ceres_data/6n28_9326/03_2026/6n28_9326_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n28_9326/03_2026/6n28_9326_neut.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 65 5.16 5 C 9110 2.51 5 N 2255 2.21 5 O 2450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13885 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2776 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 324} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E Time building chain proxies: 2.01, per 1000 atoms: 0.14 Number of scatterers: 13885 At special positions: 0 Unit cell: (95.744, 96.832, 112.064, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 65 16.00 O 2450 8.00 N 2255 7.00 C 9110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 185 " distance=2.04 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 185 " distance=2.04 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 185 " distance=2.04 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 185 " distance=2.04 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 185 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 715.8 milliseconds 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 0 sheets defined 76.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 19 through 23 removed outlier: 3.722A pdb=" N GLN A 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 33 removed outlier: 3.592A pdb=" N LEU A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 53 Processing helix chain 'A' and resid 55 through 73 removed outlier: 3.530A pdb=" N LYS A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 77 through 98 removed outlier: 3.582A pdb=" N VAL A 81 " --> pdb=" O PRO A 77 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE A 84 " --> pdb=" O PHE A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 114 removed outlier: 3.860A pdb=" N CYS A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 144 removed outlier: 3.781A pdb=" N SER A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE A 139 " --> pdb=" O CYS A 135 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 151 removed outlier: 3.611A pdb=" N TYR A 148 " --> pdb=" O SER A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 160 removed outlier: 3.672A pdb=" N VAL A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 183 through 198 removed outlier: 4.215A pdb=" N SER A 189 " --> pdb=" O CYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 removed outlier: 3.722A pdb=" N LEU A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.570A pdb=" N THR A 237 " --> pdb=" O PRO A 233 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 274 through 295 removed outlier: 3.808A pdb=" N ALA A 291 " --> pdb=" O TRP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 322 removed outlier: 3.632A pdb=" N VAL A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.721A pdb=" N GLN B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 33 removed outlier: 3.593A pdb=" N LEU B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 53 Processing helix chain 'B' and resid 55 through 73 removed outlier: 3.530A pdb=" N LYS B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 77 through 98 removed outlier: 3.582A pdb=" N VAL B 81 " --> pdb=" O PRO B 77 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE B 84 " --> pdb=" O PHE B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 114 removed outlier: 3.860A pdb=" N CYS B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 144 removed outlier: 3.781A pdb=" N SER B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE B 139 " --> pdb=" O CYS B 135 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 151 removed outlier: 3.611A pdb=" N TYR B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 160 removed outlier: 3.672A pdb=" N VAL B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 183 through 198 removed outlier: 4.215A pdb=" N SER B 189 " --> pdb=" O CYS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 230 removed outlier: 3.721A pdb=" N LEU B 207 " --> pdb=" O ASP B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 removed outlier: 3.570A pdb=" N THR B 237 " --> pdb=" O PRO B 233 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 274 through 295 removed outlier: 3.807A pdb=" N ALA B 291 " --> pdb=" O TRP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 322 removed outlier: 3.632A pdb=" N VAL B 322 " --> pdb=" O SER B 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 19 through 23 removed outlier: 3.721A pdb=" N GLN C 23 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 33 removed outlier: 3.592A pdb=" N LEU C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 53 Processing helix chain 'C' and resid 55 through 73 removed outlier: 3.530A pdb=" N LYS C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'C' and resid 77 through 98 removed outlier: 3.582A pdb=" N VAL C 81 " --> pdb=" O PRO C 77 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE C 84 " --> pdb=" O PHE C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 114 removed outlier: 3.860A pdb=" N CYS C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL C 114 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 144 removed outlier: 3.781A pdb=" N SER C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE C 139 " --> pdb=" O CYS C 135 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 151 removed outlier: 3.610A pdb=" N TYR C 148 " --> pdb=" O SER C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 160 removed outlier: 3.673A pdb=" N VAL C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 174 Processing helix chain 'C' and resid 183 through 198 removed outlier: 4.215A pdb=" N SER C 189 " --> pdb=" O CYS C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 230 removed outlier: 3.721A pdb=" N LEU C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 removed outlier: 3.569A pdb=" N THR C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 274 through 295 removed outlier: 3.807A pdb=" N ALA C 291 " --> pdb=" O TRP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 322 removed outlier: 3.632A pdb=" N VAL C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 19 through 23 removed outlier: 3.721A pdb=" N GLN D 23 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 33 removed outlier: 3.592A pdb=" N LEU D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 53 Processing helix chain 'D' and resid 55 through 73 removed outlier: 3.530A pdb=" N LYS D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 77 through 98 removed outlier: 3.582A pdb=" N VAL D 81 " --> pdb=" O PRO D 77 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE D 84 " --> pdb=" O PHE D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 114 removed outlier: 3.859A pdb=" N CYS D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 144 removed outlier: 3.781A pdb=" N SER D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE D 139 " --> pdb=" O CYS D 135 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 151 removed outlier: 3.611A pdb=" N TYR D 148 " --> pdb=" O SER D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 160 removed outlier: 3.672A pdb=" N VAL D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 174 Processing helix chain 'D' and resid 183 through 198 removed outlier: 4.215A pdb=" N SER D 189 " --> pdb=" O CYS D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 230 removed outlier: 3.721A pdb=" N LEU D 207 " --> pdb=" O ASP D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 removed outlier: 3.570A pdb=" N THR D 237 " --> pdb=" O PRO D 233 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 274 through 295 removed outlier: 3.808A pdb=" N ALA D 291 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 322 removed outlier: 3.632A pdb=" N VAL D 322 " --> pdb=" O SER D 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 9 Processing helix chain 'E' and resid 19 through 23 removed outlier: 3.722A pdb=" N GLN E 23 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 33 removed outlier: 3.593A pdb=" N LEU E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 53 Processing helix chain 'E' and resid 55 through 73 removed outlier: 3.530A pdb=" N LYS E 64 " --> pdb=" O LEU E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 77 through 98 removed outlier: 3.582A pdb=" N VAL E 81 " --> pdb=" O PRO E 77 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE E 84 " --> pdb=" O PHE E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 114 removed outlier: 3.860A pdb=" N CYS E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL E 114 " --> pdb=" O VAL E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 144 removed outlier: 3.781A pdb=" N SER E 136 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE E 139 " --> pdb=" O CYS E 135 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 151 removed outlier: 3.611A pdb=" N TYR E 148 " --> pdb=" O SER E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 160 removed outlier: 3.672A pdb=" N VAL E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 174 Processing helix chain 'E' and resid 183 through 198 removed outlier: 4.215A pdb=" N SER E 189 " --> pdb=" O CYS E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 230 removed outlier: 3.722A pdb=" N LEU E 207 " --> pdb=" O ASP E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 removed outlier: 3.569A pdb=" N THR E 237 " --> pdb=" O PRO E 233 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 274 through 295 removed outlier: 3.808A pdb=" N ALA E 291 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 322 removed outlier: 3.632A pdb=" N VAL E 322 " --> pdb=" O SER E 318 " (cutoff:3.500A) 860 hydrogen bonds defined for protein. 2505 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.04 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4296 1.34 - 1.46: 3762 1.46 - 1.59: 6112 1.59 - 1.71: 0 1.71 - 1.83: 100 Bond restraints: 14270 Sorted by residual: bond pdb=" CB VAL D 81 " pdb=" CG1 VAL D 81 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.37e+00 bond pdb=" CB VAL C 81 " pdb=" CG1 VAL C 81 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.37e+00 bond pdb=" CB VAL A 81 " pdb=" CG1 VAL A 81 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.32e+00 bond pdb=" CB VAL B 81 " pdb=" CG1 VAL B 81 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.32e+00 bond pdb=" CB VAL E 81 " pdb=" CG1 VAL E 81 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.28e+00 ... (remaining 14265 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 18376 1.58 - 3.17: 895 3.17 - 4.75: 124 4.75 - 6.33: 20 6.33 - 7.92: 20 Bond angle restraints: 19435 Sorted by residual: angle pdb=" C LEU D 271 " pdb=" N PHE D 272 " pdb=" CA PHE D 272 " ideal model delta sigma weight residual 121.54 128.31 -6.77 1.91e+00 2.74e-01 1.26e+01 angle pdb=" C LEU C 271 " pdb=" N PHE C 272 " pdb=" CA PHE C 272 " ideal model delta sigma weight residual 121.54 128.27 -6.73 1.91e+00 2.74e-01 1.24e+01 angle pdb=" C LEU A 271 " pdb=" N PHE A 272 " pdb=" CA PHE A 272 " ideal model delta sigma weight residual 121.54 128.27 -6.73 1.91e+00 2.74e-01 1.24e+01 angle pdb=" C LEU E 271 " pdb=" N PHE E 272 " pdb=" CA PHE E 272 " ideal model delta sigma weight residual 121.54 128.26 -6.72 1.91e+00 2.74e-01 1.24e+01 angle pdb=" C LEU B 271 " pdb=" N PHE B 272 " pdb=" CA PHE B 272 " ideal model delta sigma weight residual 121.54 128.24 -6.70 1.91e+00 2.74e-01 1.23e+01 ... (remaining 19430 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.93: 7950 14.93 - 29.86: 270 29.86 - 44.79: 90 44.79 - 59.72: 10 59.72 - 74.65: 10 Dihedral angle restraints: 8330 sinusoidal: 3310 harmonic: 5020 Sorted by residual: dihedral pdb=" CA PRO B 103 " pdb=" C PRO B 103 " pdb=" N ASP B 104 " pdb=" CA ASP B 104 " ideal model delta harmonic sigma weight residual 180.00 -158.56 -21.44 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA PRO A 103 " pdb=" C PRO A 103 " pdb=" N ASP A 104 " pdb=" CA ASP A 104 " ideal model delta harmonic sigma weight residual -180.00 -158.60 -21.40 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA PRO E 103 " pdb=" C PRO E 103 " pdb=" N ASP E 104 " pdb=" CA ASP E 104 " ideal model delta harmonic sigma weight residual -180.00 -158.62 -21.38 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 8327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1296 0.041 - 0.082: 633 0.082 - 0.124: 176 0.124 - 0.165: 15 0.165 - 0.206: 30 Chirality restraints: 2150 Sorted by residual: chirality pdb=" CG LEU D 258 " pdb=" CB LEU D 258 " pdb=" CD1 LEU D 258 " pdb=" CD2 LEU D 258 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CG LEU E 258 " pdb=" CB LEU E 258 " pdb=" CD1 LEU E 258 " pdb=" CD2 LEU E 258 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CG LEU B 258 " pdb=" CB LEU B 258 " pdb=" CD1 LEU B 258 " pdb=" CD2 LEU B 258 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 2147 not shown) Planarity restraints: 2430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 282 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.09e+00 pdb=" C PHE C 282 " 0.035 2.00e-02 2.50e+03 pdb=" O PHE C 282 " -0.013 2.00e-02 2.50e+03 pdb=" N PHE C 283 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 282 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.06e+00 pdb=" C PHE D 282 " -0.035 2.00e-02 2.50e+03 pdb=" O PHE D 282 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE D 283 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 282 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.04e+00 pdb=" C PHE A 282 " -0.035 2.00e-02 2.50e+03 pdb=" O PHE A 282 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE A 283 " 0.012 2.00e-02 2.50e+03 ... (remaining 2427 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1731 2.75 - 3.29: 13096 3.29 - 3.83: 23531 3.83 - 4.36: 27752 4.36 - 4.90: 48778 Nonbonded interactions: 114888 Sorted by model distance: nonbonded pdb=" O ASN C 296 " pdb="CA CA C 401 " model vdw 2.215 2.510 nonbonded pdb=" O ASN B 296 " pdb="CA CA B 401 " model vdw 2.215 2.510 nonbonded pdb=" O ASN E 296 " pdb="CA CA E 401 " model vdw 2.215 2.510 nonbonded pdb=" O ASN A 296 " pdb="CA CA A 401 " model vdw 2.215 2.510 nonbonded pdb=" O ASN D 296 " pdb="CA CA D 401 " model vdw 2.216 2.510 ... (remaining 114883 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.420 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 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 : 0.006 0.051 14275 Z= 0.258 Angle : 0.782 7.915 19445 Z= 0.433 Chirality : 0.052 0.206 2150 Planarity : 0.007 0.045 2430 Dihedral : 9.537 74.652 5075 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.44 (0.15), residues: 1680 helix: -1.88 (0.11), residues: 1135 sheet: None (None), residues: 0 loop : -2.86 (0.21), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 313 TYR 0.011 0.002 TYR E 97 PHE 0.021 0.003 PHE E 283 TRP 0.028 0.003 TRP C 94 HIS 0.009 0.003 HIS C 326 Details of bonding type rmsd covalent geometry : bond 0.00613 (14270) covalent geometry : angle 0.77952 (19435) SS BOND : bond 0.00451 ( 5) SS BOND : angle 2.83384 ( 10) hydrogen bonds : bond 0.13898 ( 860) hydrogen bonds : angle 5.86900 ( 2505) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.541 Fit side-chains REVERT: A 58 GLN cc_start: 0.8567 (mt0) cc_final: 0.8328 (mt0) REVERT: B 18 SER cc_start: 0.9041 (m) cc_final: 0.8767 (t) REVERT: B 58 GLN cc_start: 0.8517 (mt0) cc_final: 0.8309 (mt0) REVERT: B 129 MET cc_start: 0.9092 (mmm) cc_final: 0.8887 (mmt) REVERT: B 320 MET cc_start: 0.8599 (ttt) cc_final: 0.8300 (ttm) REVERT: C 18 SER cc_start: 0.8999 (m) cc_final: 0.8625 (t) REVERT: C 175 ASN cc_start: 0.8384 (t0) cc_final: 0.8178 (t0) REVERT: C 249 LEU cc_start: 0.9206 (tp) cc_final: 0.8985 (mm) REVERT: D 249 LEU cc_start: 0.9264 (tp) cc_final: 0.9031 (mm) REVERT: D 334 LYS cc_start: 0.8731 (mttt) cc_final: 0.8459 (mttp) REVERT: E 18 SER cc_start: 0.9101 (m) cc_final: 0.8783 (t) REVERT: E 58 GLN cc_start: 0.8598 (mt0) cc_final: 0.8381 (mt0) REVERT: E 334 LYS cc_start: 0.8793 (mttt) cc_final: 0.8571 (mmtp) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.6702 time to fit residues: 197.0332 Evaluate side-chains 125 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN A 293 GLN B 19 GLN B 133 ASN B 293 GLN D 58 GLN D 256 GLN E 256 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.089646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.071775 restraints weight = 21959.679| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 2.13 r_work: 0.2672 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14275 Z= 0.139 Angle : 0.517 7.633 19445 Z= 0.271 Chirality : 0.039 0.162 2150 Planarity : 0.004 0.032 2430 Dihedral : 3.944 15.000 1875 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.65 % Allowed : 8.98 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.19), residues: 1680 helix: 0.08 (0.14), residues: 1195 sheet: None (None), residues: 0 loop : -2.39 (0.25), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 159 TYR 0.018 0.001 TYR D 97 PHE 0.012 0.001 PHE C 281 TRP 0.016 0.002 TRP D 94 HIS 0.003 0.001 HIS C 326 Details of bonding type rmsd covalent geometry : bond 0.00315 (14270) covalent geometry : angle 0.51610 (19435) SS BOND : bond 0.00452 ( 5) SS BOND : angle 1.29449 ( 10) hydrogen bonds : bond 0.04847 ( 860) hydrogen bonds : angle 4.23944 ( 2505) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.504 Fit side-chains REVERT: A 303 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8469 (t70) REVERT: B 58 GLN cc_start: 0.8572 (mt0) cc_final: 0.8190 (mt0) REVERT: B 196 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8507 (tpt-90) REVERT: B 320 MET cc_start: 0.9043 (ttt) cc_final: 0.8822 (ttm) REVERT: C 61 MET cc_start: 0.7039 (OUTLIER) cc_final: 0.6542 (ttp) REVERT: E 18 SER cc_start: 0.9315 (m) cc_final: 0.8894 (t) REVERT: E 58 GLN cc_start: 0.8536 (mt0) cc_final: 0.8128 (mt0) REVERT: E 65 LEU cc_start: 0.8913 (tp) cc_final: 0.8561 (tp) REVERT: E 149 LYS cc_start: 0.8934 (mttm) cc_final: 0.8664 (mttm) REVERT: E 333 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7598 (mm-30) outliers start: 25 outliers final: 3 residues processed: 153 average time/residue: 0.5643 time to fit residues: 94.7837 Evaluate side-chains 111 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 8 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 11 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN B 19 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.094101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.076329 restraints weight = 21725.365| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.12 r_work: 0.2755 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14275 Z= 0.097 Angle : 0.456 6.394 19445 Z= 0.237 Chirality : 0.037 0.158 2150 Planarity : 0.003 0.026 2430 Dihedral : 3.551 13.582 1875 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.78 % Allowed : 9.04 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.20), residues: 1680 helix: 1.11 (0.15), residues: 1190 sheet: None (None), residues: 0 loop : -2.15 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 159 TYR 0.014 0.001 TYR D 97 PHE 0.009 0.001 PHE B 171 TRP 0.013 0.001 TRP E 94 HIS 0.003 0.000 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00203 (14270) covalent geometry : angle 0.45601 (19435) SS BOND : bond 0.00210 ( 5) SS BOND : angle 0.76945 ( 10) hydrogen bonds : bond 0.03912 ( 860) hydrogen bonds : angle 3.91072 ( 2505) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.563 Fit side-chains REVERT: A 61 MET cc_start: 0.8297 (tpt) cc_final: 0.8056 (ttp) REVERT: B 58 GLN cc_start: 0.8452 (mt0) cc_final: 0.7757 (mt0) REVERT: B 196 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8468 (tpt-90) REVERT: C 196 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8436 (tpt-90) REVERT: D 18 SER cc_start: 0.9303 (m) cc_final: 0.8959 (t) REVERT: D 262 LYS cc_start: 0.8694 (mmtm) cc_final: 0.8491 (mttm) REVERT: E 18 SER cc_start: 0.9219 (m) cc_final: 0.8863 (t) REVERT: E 58 GLN cc_start: 0.8417 (mt0) cc_final: 0.8064 (mt0) REVERT: E 65 LEU cc_start: 0.8809 (tp) cc_final: 0.8431 (tp) REVERT: E 149 LYS cc_start: 0.8977 (mttm) cc_final: 0.8713 (mttm) REVERT: E 203 ASP cc_start: 0.8234 (m-30) cc_final: 0.8018 (m-30) REVERT: E 333 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7560 (mm-30) outliers start: 27 outliers final: 7 residues processed: 150 average time/residue: 0.6102 time to fit residues: 100.1734 Evaluate side-chains 110 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 41 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 22 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 163 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 2 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.091245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.073229 restraints weight = 21815.240| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.09 r_work: 0.2708 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14275 Z= 0.123 Angle : 0.469 8.256 19445 Z= 0.244 Chirality : 0.038 0.159 2150 Planarity : 0.003 0.031 2430 Dihedral : 3.473 13.058 1875 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.38 % Allowed : 9.83 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.20), residues: 1680 helix: 1.40 (0.15), residues: 1215 sheet: None (None), residues: 0 loop : -2.25 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 159 TYR 0.019 0.001 TYR B 97 PHE 0.010 0.001 PHE C 281 TRP 0.013 0.001 TRP D 94 HIS 0.003 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00282 (14270) covalent geometry : angle 0.46888 (19435) SS BOND : bond 0.00306 ( 5) SS BOND : angle 1.02959 ( 10) hydrogen bonds : bond 0.04327 ( 860) hydrogen bonds : angle 3.83372 ( 2505) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.557 Fit side-chains REVERT: A 61 MET cc_start: 0.8403 (tpt) cc_final: 0.8100 (ttp) REVERT: B 58 GLN cc_start: 0.8483 (mt0) cc_final: 0.7873 (mt0) REVERT: B 196 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8508 (tpt-90) REVERT: B 333 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7638 (mt-10) REVERT: C 196 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8412 (tpt-90) REVERT: D 18 SER cc_start: 0.9342 (m) cc_final: 0.9065 (t) REVERT: D 196 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8015 (tpt-90) REVERT: E 18 SER cc_start: 0.9242 (m) cc_final: 0.8998 (t) REVERT: E 65 LEU cc_start: 0.8862 (tp) cc_final: 0.8486 (tp) REVERT: E 149 LYS cc_start: 0.8935 (mttm) cc_final: 0.8687 (mttm) REVERT: E 203 ASP cc_start: 0.8266 (m-30) cc_final: 0.8042 (m-30) REVERT: E 333 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7723 (mm-30) outliers start: 36 outliers final: 13 residues processed: 138 average time/residue: 0.5781 time to fit residues: 87.6805 Evaluate side-chains 114 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 196 ARG Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 29 optimal weight: 0.1980 chunk 98 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 50 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.090747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.072649 restraints weight = 21960.133| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.09 r_work: 0.2694 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14275 Z= 0.129 Angle : 0.468 7.668 19445 Z= 0.245 Chirality : 0.038 0.159 2150 Planarity : 0.003 0.027 2430 Dihedral : 3.474 13.286 1875 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.44 % Allowed : 10.03 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.21), residues: 1680 helix: 1.56 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : -2.10 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 218 TYR 0.018 0.001 TYR B 97 PHE 0.009 0.001 PHE C 248 TRP 0.011 0.001 TRP D 94 HIS 0.003 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00297 (14270) covalent geometry : angle 0.46792 (19435) SS BOND : bond 0.00305 ( 5) SS BOND : angle 1.06145 ( 10) hydrogen bonds : bond 0.04376 ( 860) hydrogen bonds : angle 3.79775 ( 2505) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 0.589 Fit side-chains REVERT: A 61 MET cc_start: 0.8440 (tpt) cc_final: 0.8135 (ttp) REVERT: A 196 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.5859 (tpt-90) REVERT: B 196 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8476 (tpt-90) REVERT: B 333 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7688 (mt-10) REVERT: C 61 MET cc_start: 0.7073 (OUTLIER) cc_final: 0.6531 (ttp) REVERT: C 196 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8412 (tpt-90) REVERT: C 262 LYS cc_start: 0.8385 (mmtp) cc_final: 0.8159 (mmtm) REVERT: D 18 SER cc_start: 0.9361 (m) cc_final: 0.9087 (t) REVERT: D 196 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8042 (tpt-90) REVERT: E 65 LEU cc_start: 0.8831 (tp) cc_final: 0.8463 (tp) REVERT: E 149 LYS cc_start: 0.8928 (mttm) cc_final: 0.8696 (mttm) REVERT: E 203 ASP cc_start: 0.8286 (m-30) cc_final: 0.8038 (m-30) REVERT: E 333 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7662 (mm-30) outliers start: 37 outliers final: 15 residues processed: 137 average time/residue: 0.5721 time to fit residues: 86.3953 Evaluate side-chains 124 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain D residue 196 ARG Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 91 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 130 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.089331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.070928 restraints weight = 21807.734| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 2.08 r_work: 0.2651 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2514 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14275 Z= 0.150 Angle : 0.494 8.218 19445 Z= 0.256 Chirality : 0.039 0.159 2150 Planarity : 0.003 0.028 2430 Dihedral : 3.527 13.876 1875 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.57 % Allowed : 10.63 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.21), residues: 1680 helix: 1.59 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : -1.89 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 218 TYR 0.020 0.001 TYR B 97 PHE 0.017 0.001 PHE E 272 TRP 0.011 0.001 TRP D 94 HIS 0.003 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00351 (14270) covalent geometry : angle 0.49291 (19435) SS BOND : bond 0.00368 ( 5) SS BOND : angle 1.19983 ( 10) hydrogen bonds : bond 0.04683 ( 860) hydrogen bonds : angle 3.85850 ( 2505) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 109 time to evaluate : 0.551 Fit side-chains REVERT: A 61 MET cc_start: 0.8476 (tpt) cc_final: 0.8157 (ttp) REVERT: B 196 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8498 (tpt-90) REVERT: B 333 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7703 (mt-10) REVERT: C 61 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6634 (ttp) REVERT: C 196 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8408 (tpt-90) REVERT: C 262 LYS cc_start: 0.8386 (mmtp) cc_final: 0.8162 (mmtm) REVERT: D 18 SER cc_start: 0.9363 (m) cc_final: 0.9080 (t) REVERT: D 196 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8075 (tpt-90) REVERT: E 65 LEU cc_start: 0.8849 (tp) cc_final: 0.8481 (tp) REVERT: E 149 LYS cc_start: 0.8898 (mttm) cc_final: 0.8663 (mttm) REVERT: E 196 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.7534 (tmt90) REVERT: E 203 ASP cc_start: 0.8208 (m-30) cc_final: 0.7907 (m-30) outliers start: 39 outliers final: 17 residues processed: 137 average time/residue: 0.5727 time to fit residues: 86.3569 Evaluate side-chains 124 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 196 ARG Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 196 ARG Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 164 optimal weight: 10.0000 chunk 161 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 150 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN B 58 GLN B 293 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.088906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.070403 restraints weight = 21819.369| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 2.08 r_work: 0.2645 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2508 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14275 Z= 0.158 Angle : 0.502 7.518 19445 Z= 0.260 Chirality : 0.040 0.160 2150 Planarity : 0.003 0.030 2430 Dihedral : 3.557 13.940 1875 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.18 % Allowed : 11.22 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.21), residues: 1680 helix: 1.60 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : -1.87 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 218 TYR 0.020 0.001 TYR B 97 PHE 0.018 0.001 PHE E 272 TRP 0.011 0.001 TRP D 94 HIS 0.003 0.001 HIS C 326 Details of bonding type rmsd covalent geometry : bond 0.00372 (14270) covalent geometry : angle 0.50146 (19435) SS BOND : bond 0.00388 ( 5) SS BOND : angle 1.25989 ( 10) hydrogen bonds : bond 0.04757 ( 860) hydrogen bonds : angle 3.88720 ( 2505) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.578 Fit side-chains REVERT: A 61 MET cc_start: 0.8490 (tpt) cc_final: 0.8152 (ttp) REVERT: B 196 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8558 (tpt-90) REVERT: C 196 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8365 (tpt-90) REVERT: C 262 LYS cc_start: 0.8474 (mmtp) cc_final: 0.8273 (mmtt) REVERT: D 18 SER cc_start: 0.9337 (m) cc_final: 0.9066 (t) REVERT: E 65 LEU cc_start: 0.8843 (tp) cc_final: 0.8498 (tp) REVERT: E 149 LYS cc_start: 0.8913 (mttm) cc_final: 0.8668 (mttm) REVERT: E 196 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.7534 (tmt90) REVERT: E 203 ASP cc_start: 0.8226 (m-30) cc_final: 0.7907 (m-30) outliers start: 33 outliers final: 15 residues processed: 126 average time/residue: 0.5761 time to fit residues: 79.6692 Evaluate side-chains 116 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 196 ARG Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 67 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 145 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.088086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.069546 restraints weight = 21821.204| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 2.08 r_work: 0.2631 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2492 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14275 Z= 0.174 Angle : 0.527 7.946 19445 Z= 0.272 Chirality : 0.040 0.159 2150 Planarity : 0.003 0.031 2430 Dihedral : 3.608 13.938 1875 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.85 % Allowed : 11.82 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.21), residues: 1680 helix: 1.76 (0.15), residues: 1190 sheet: None (None), residues: 0 loop : -1.70 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 218 TYR 0.021 0.001 TYR B 97 PHE 0.019 0.002 PHE E 272 TRP 0.011 0.001 TRP D 94 HIS 0.004 0.001 HIS C 326 Details of bonding type rmsd covalent geometry : bond 0.00415 (14270) covalent geometry : angle 0.52610 (19435) SS BOND : bond 0.00430 ( 5) SS BOND : angle 1.34294 ( 10) hydrogen bonds : bond 0.04933 ( 860) hydrogen bonds : angle 3.93181 ( 2505) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.423 Fit side-chains REVERT: A 61 MET cc_start: 0.8510 (tpt) cc_final: 0.8109 (ptt) REVERT: B 196 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8554 (tpt-90) REVERT: C 196 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8358 (tpt-90) REVERT: C 262 LYS cc_start: 0.8458 (mmtp) cc_final: 0.8234 (mmtt) REVERT: D 18 SER cc_start: 0.9331 (m) cc_final: 0.9062 (t) REVERT: D 196 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8029 (tpt-90) REVERT: E 65 LEU cc_start: 0.8858 (tp) cc_final: 0.8511 (tp) REVERT: E 149 LYS cc_start: 0.8891 (mttm) cc_final: 0.8677 (mttp) REVERT: E 196 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.7445 (tmt90) REVERT: E 203 ASP cc_start: 0.8187 (m-30) cc_final: 0.7874 (m-30) outliers start: 28 outliers final: 14 residues processed: 121 average time/residue: 0.6131 time to fit residues: 81.1502 Evaluate side-chains 116 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 196 ARG Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 196 ARG Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 97 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 chunk 157 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 60 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN B 293 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.088814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.070168 restraints weight = 21864.653| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 2.09 r_work: 0.2635 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14275 Z= 0.159 Angle : 0.498 7.844 19445 Z= 0.257 Chirality : 0.040 0.160 2150 Planarity : 0.003 0.028 2430 Dihedral : 3.598 13.742 1875 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.58 % Allowed : 12.28 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.21), residues: 1680 helix: 1.76 (0.15), residues: 1190 sheet: None (None), residues: 0 loop : -1.69 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 196 TYR 0.020 0.001 TYR B 97 PHE 0.021 0.001 PHE E 272 TRP 0.011 0.001 TRP D 94 HIS 0.003 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00376 (14270) covalent geometry : angle 0.49722 (19435) SS BOND : bond 0.00392 ( 5) SS BOND : angle 1.26986 ( 10) hydrogen bonds : bond 0.04805 ( 860) hydrogen bonds : angle 3.91592 ( 2505) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.663 Fit side-chains REVERT: A 61 MET cc_start: 0.8529 (tpt) cc_final: 0.8168 (ttp) REVERT: B 196 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8546 (tpt-90) REVERT: C 196 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8364 (tpt-90) REVERT: C 262 LYS cc_start: 0.8500 (mmtp) cc_final: 0.8219 (mmtt) REVERT: D 18 SER cc_start: 0.9321 (m) cc_final: 0.9059 (t) REVERT: D 196 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8030 (tpt-90) REVERT: E 65 LEU cc_start: 0.8838 (tp) cc_final: 0.8477 (tp) REVERT: E 149 LYS cc_start: 0.8906 (mttm) cc_final: 0.8687 (mttp) REVERT: E 196 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.7471 (tmt90) REVERT: E 203 ASP cc_start: 0.8195 (m-30) cc_final: 0.7879 (m-30) REVERT: E 334 LYS cc_start: 0.9041 (mttt) cc_final: 0.8124 (mmtp) outliers start: 24 outliers final: 14 residues processed: 116 average time/residue: 0.5810 time to fit residues: 74.1186 Evaluate side-chains 115 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 196 ARG Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 196 ARG Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 16 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 91 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 chunk 101 optimal weight: 0.0270 chunk 111 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 overall best weight: 2.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN B 293 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.088923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.070409 restraints weight = 21658.967| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 2.07 r_work: 0.2644 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14275 Z= 0.149 Angle : 0.491 7.796 19445 Z= 0.254 Chirality : 0.039 0.160 2150 Planarity : 0.003 0.028 2430 Dihedral : 3.576 13.785 1875 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.65 % Allowed : 12.28 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.21), residues: 1680 helix: 1.80 (0.15), residues: 1190 sheet: None (None), residues: 0 loop : -1.69 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 196 TYR 0.019 0.001 TYR B 97 PHE 0.023 0.001 PHE E 272 TRP 0.011 0.001 TRP D 94 HIS 0.003 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00350 (14270) covalent geometry : angle 0.49057 (19435) SS BOND : bond 0.00387 ( 5) SS BOND : angle 1.22428 ( 10) hydrogen bonds : bond 0.04684 ( 860) hydrogen bonds : angle 3.89393 ( 2505) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.554 Fit side-chains REVERT: A 61 MET cc_start: 0.8522 (tpt) cc_final: 0.8144 (ttp) REVERT: B 196 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8534 (tpt-90) REVERT: C 196 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8396 (tpt-90) REVERT: C 262 LYS cc_start: 0.8503 (mmtp) cc_final: 0.8219 (mmtt) REVERT: D 18 SER cc_start: 0.9325 (m) cc_final: 0.9035 (t) REVERT: E 65 LEU cc_start: 0.8831 (tp) cc_final: 0.8472 (tp) REVERT: E 149 LYS cc_start: 0.8888 (mttm) cc_final: 0.8666 (mttp) REVERT: E 196 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.7351 (tmt90) REVERT: E 203 ASP cc_start: 0.8168 (m-30) cc_final: 0.7845 (m-30) REVERT: E 334 LYS cc_start: 0.9050 (mttt) cc_final: 0.8115 (mmtp) outliers start: 25 outliers final: 13 residues processed: 120 average time/residue: 0.5833 time to fit residues: 76.8513 Evaluate side-chains 116 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 196 ARG Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 21 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.090291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.071645 restraints weight = 21678.412| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 2.09 r_work: 0.2671 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14275 Z= 0.129 Angle : 0.474 7.708 19445 Z= 0.246 Chirality : 0.039 0.158 2150 Planarity : 0.003 0.028 2430 Dihedral : 3.515 13.208 1875 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.25 % Allowed : 12.67 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.21), residues: 1680 helix: 1.86 (0.15), residues: 1190 sheet: None (None), residues: 0 loop : -1.68 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 196 TYR 0.017 0.001 TYR B 97 PHE 0.025 0.001 PHE E 272 TRP 0.012 0.001 TRP D 94 HIS 0.003 0.001 HIS C 326 Details of bonding type rmsd covalent geometry : bond 0.00295 (14270) covalent geometry : angle 0.47330 (19435) SS BOND : bond 0.00329 ( 5) SS BOND : angle 1.09029 ( 10) hydrogen bonds : bond 0.04404 ( 860) hydrogen bonds : angle 3.85606 ( 2505) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3643.02 seconds wall clock time: 62 minutes 51.21 seconds (3771.21 seconds total)