Starting phenix.real_space_refine on Fri Jul 3 23:36:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jzl_61917/07_2026/9jzl_61917.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jzl_61917/07_2026/9jzl_61917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jzl_61917/07_2026/9jzl_61917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jzl_61917/07_2026/9jzl_61917.map" model { file = "/net/cci-nas-00/data/ceres_data/9jzl_61917/07_2026/9jzl_61917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jzl_61917/07_2026/9jzl_61917.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.089 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 P 48 5.49 5 S 84 5.16 5 C 10570 2.51 5 N 2814 2.21 5 O 3322 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16838 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2634 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 19, 'TRANS': 319} Chain breaks: 1 Chain: "B" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2664 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 19, 'TRANS': 323} Chain breaks: 1 Chain: "C" Number of atoms: 2641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2641 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 19, 'TRANS': 320} Chain breaks: 1 Chain: "R" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 480 Classifications: {'RNA': 24} Modifications used: {'rna2p_pyr': 3, 'rna3p_pyr': 21} Link IDs: {'rna2p': 3, 'rna3p': 20} Restraints were copied for chains: D, E, F, G Time building chain proxies: 4.28, per 1000 atoms: 0.25 Number of scatterers: 16838 At special positions: 0 Unit cell: (134.922, 134.922, 100.296, 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) S 84 16.00 P 48 15.00 O 3322 8.00 N 2814 7.00 C 10570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 584.5 milliseconds 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3800 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 6 sheets defined 67.0% alpha, 1.3% beta 0 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 62 through 69 removed outlier: 3.525A pdb=" N ARG A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N MET A 68 " --> pdb=" O SER A 64 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE A 69 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 83 removed outlier: 4.722A pdb=" N SER A 75 " --> pdb=" O THR A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 94 removed outlier: 3.893A pdb=" N ALA A 89 " --> pdb=" O GLY A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 150 Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 159 through 173 removed outlier: 3.631A pdb=" N LYS A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 182 removed outlier: 3.587A pdb=" N GLY A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU A 180 " --> pdb=" O PRO A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 200 Processing helix chain 'A' and resid 202 through 213 Processing helix chain 'A' and resid 216 through 231 removed outlier: 3.842A pdb=" N GLU A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 245 Processing helix chain 'A' and resid 250 through 254 removed outlier: 4.058A pdb=" N LEU A 253 " --> pdb=" O ASP A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 277 Processing helix chain 'A' and resid 278 through 283 Proline residue: A 281 - end of helix No H-bonds generated for 'chain 'A' and resid 278 through 283' Processing helix chain 'A' and resid 288 through 298 Proline residue: A 296 - end of helix Processing helix chain 'A' and resid 299 through 314 removed outlier: 3.665A pdb=" N LYS A 312 " --> pdb=" O TYR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 320 Processing helix chain 'A' and resid 332 through 342 removed outlier: 3.921A pdb=" N ARG A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 52 through 61 Processing helix chain 'B' and resid 62 through 69 removed outlier: 3.794A pdb=" N ARG B 66 " --> pdb=" O ASP B 62 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET B 68 " --> pdb=" O SER B 64 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE B 69 " --> pdb=" O ARG B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 83 removed outlier: 4.633A pdb=" N SER B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 93 removed outlier: 3.802A pdb=" N ALA B 89 " --> pdb=" O GLY B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 150 removed outlier: 3.769A pdb=" N GLY B 146 " --> pdb=" O SER B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 159 through 173 removed outlier: 3.939A pdb=" N LYS B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 190 through 200 Processing helix chain 'B' and resid 202 through 212 Processing helix chain 'B' and resid 216 through 231 removed outlier: 3.786A pdb=" N GLU B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 248 Processing helix chain 'B' and resid 250 through 254 removed outlier: 4.023A pdb=" N LEU B 253 " --> pdb=" O ASP B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 276 removed outlier: 3.548A pdb=" N ARG B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP B 264 " --> pdb=" O TYR B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 283 Processing helix chain 'B' and resid 288 through 295 Processing helix chain 'B' and resid 299 through 314 Processing helix chain 'B' and resid 315 through 320 Processing helix chain 'B' and resid 332 through 342 removed outlier: 4.127A pdb=" N ARG B 342 " --> pdb=" O ARG B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 365 Processing helix chain 'C' and resid 49 through 51 No H-bonds generated for 'chain 'C' and resid 49 through 51' Processing helix chain 'C' and resid 52 through 61 removed outlier: 3.583A pdb=" N ALA C 57 " --> pdb=" O ILE C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 69 removed outlier: 3.597A pdb=" N PHE C 69 " --> pdb=" O ARG C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 83 removed outlier: 4.470A pdb=" N SER C 75 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 93 removed outlier: 3.786A pdb=" N ALA C 89 " --> pdb=" O GLY C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 150 Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 159 through 173 removed outlier: 3.608A pdb=" N LYS C 163 " --> pdb=" O ALA C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 182 Processing helix chain 'C' and resid 190 through 200 Processing helix chain 'C' and resid 202 through 212 Processing helix chain 'C' and resid 216 through 231 removed outlier: 3.759A pdb=" N GLU C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 248 Processing helix chain 'C' and resid 255 through 276 removed outlier: 3.706A pdb=" N ARG C 263 " --> pdb=" O ALA C 259 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP C 264 " --> pdb=" O TYR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 283 Processing helix chain 'C' and resid 288 through 295 Processing helix chain 'C' and resid 299 through 314 Processing helix chain 'C' and resid 315 through 320 Processing helix chain 'C' and resid 332 through 342 removed outlier: 3.887A pdb=" N ARG C 342 " --> pdb=" O ARG C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 365 Processing helix chain 'D' and resid 52 through 61 Processing helix chain 'D' and resid 62 through 69 removed outlier: 3.525A pdb=" N ARG D 66 " --> pdb=" O ASP D 62 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N MET D 68 " --> pdb=" O SER D 64 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE D 69 " --> pdb=" O ARG D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 83 removed outlier: 4.722A pdb=" N SER D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 94 removed outlier: 3.893A pdb=" N ALA D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 150 Processing helix chain 'D' and resid 152 through 157 Processing helix chain 'D' and resid 159 through 173 removed outlier: 3.631A pdb=" N LYS D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 182 removed outlier: 3.587A pdb=" N GLY D 179 " --> pdb=" O ARG D 175 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU D 180 " --> pdb=" O PRO D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 200 Processing helix chain 'D' and resid 202 through 213 Processing helix chain 'D' and resid 216 through 231 removed outlier: 3.842A pdb=" N GLU D 221 " --> pdb=" O SER D 217 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE D 222 " --> pdb=" O PRO D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 245 Processing helix chain 'D' and resid 250 through 254 removed outlier: 4.058A pdb=" N LEU D 253 " --> pdb=" O ASP D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 277 Processing helix chain 'D' and resid 278 through 283 Proline residue: D 281 - end of helix No H-bonds generated for 'chain 'D' and resid 278 through 283' Processing helix chain 'D' and resid 288 through 298 Proline residue: D 296 - end of helix Processing helix chain 'D' and resid 299 through 314 removed outlier: 3.665A pdb=" N LYS D 312 " --> pdb=" O TYR D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 320 Processing helix chain 'D' and resid 332 through 342 removed outlier: 3.921A pdb=" N ARG D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 365 Processing helix chain 'E' and resid 49 through 51 No H-bonds generated for 'chain 'E' and resid 49 through 51' Processing helix chain 'E' and resid 52 through 61 Processing helix chain 'E' and resid 62 through 69 removed outlier: 3.794A pdb=" N ARG E 66 " --> pdb=" O ASP E 62 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET E 68 " --> pdb=" O SER E 64 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE E 69 " --> pdb=" O ARG E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 83 removed outlier: 4.633A pdb=" N SER E 75 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 93 removed outlier: 3.802A pdb=" N ALA E 89 " --> pdb=" O GLY E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 150 removed outlier: 3.769A pdb=" N GLY E 146 " --> pdb=" O SER E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 157 Processing helix chain 'E' and resid 159 through 173 removed outlier: 3.939A pdb=" N LYS E 163 " --> pdb=" O ALA E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 182 Processing helix chain 'E' and resid 190 through 200 Processing helix chain 'E' and resid 202 through 212 Processing helix chain 'E' and resid 216 through 231 removed outlier: 3.786A pdb=" N GLU E 221 " --> pdb=" O SER E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 248 Processing helix chain 'E' and resid 250 through 254 removed outlier: 4.023A pdb=" N LEU E 253 " --> pdb=" O ASP E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 276 removed outlier: 3.548A pdb=" N ARG E 263 " --> pdb=" O ALA E 259 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP E 264 " --> pdb=" O TYR E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 283 Processing helix chain 'E' and resid 288 through 295 Processing helix chain 'E' and resid 299 through 314 Processing helix chain 'E' and resid 315 through 320 Processing helix chain 'E' and resid 332 through 342 removed outlier: 4.127A pdb=" N ARG E 342 " --> pdb=" O ARG E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 365 Processing helix chain 'F' and resid 49 through 51 No H-bonds generated for 'chain 'F' and resid 49 through 51' Processing helix chain 'F' and resid 52 through 61 removed outlier: 3.583A pdb=" N ALA F 57 " --> pdb=" O ILE F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 69 removed outlier: 3.597A pdb=" N PHE F 69 " --> pdb=" O ARG F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 83 removed outlier: 4.470A pdb=" N SER F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 93 removed outlier: 3.786A pdb=" N ALA F 89 " --> pdb=" O GLY F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 150 Processing helix chain 'F' and resid 152 through 157 Processing helix chain 'F' and resid 159 through 173 removed outlier: 3.608A pdb=" N LYS F 163 " --> pdb=" O ALA F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 182 Processing helix chain 'F' and resid 190 through 200 Processing helix chain 'F' and resid 202 through 212 Processing helix chain 'F' and resid 216 through 231 removed outlier: 3.759A pdb=" N GLU F 221 " --> pdb=" O SER F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 248 Processing helix chain 'F' and resid 255 through 276 removed outlier: 3.706A pdb=" N ARG F 263 " --> pdb=" O ALA F 259 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP F 264 " --> pdb=" O TYR F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 283 Processing helix chain 'F' and resid 288 through 295 Processing helix chain 'F' and resid 299 through 314 Processing helix chain 'F' and resid 315 through 320 Processing helix chain 'F' and resid 332 through 342 removed outlier: 3.887A pdb=" N ARG F 342 " --> pdb=" O ARG F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 365 Processing sheet with id=1, first strand: chain 'A' and resid 99 through 100 Processing sheet with id=2, first strand: chain 'B' and resid 99 through 105 removed outlier: 3.613A pdb=" N LEU B 101 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL B 113 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'C' and resid 99 through 100 Processing sheet with id=4, first strand: chain 'D' and resid 99 through 100 Processing sheet with id=5, first strand: chain 'E' and resid 99 through 105 removed outlier: 3.613A pdb=" N LEU E 101 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL E 113 " --> pdb=" O LEU E 101 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'F' and resid 99 through 100 840 hydrogen bonds defined for protein. 2322 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 2.86 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3354 1.33 - 1.46: 4956 1.46 - 1.58: 8736 1.58 - 1.70: 96 1.70 - 1.83: 144 Bond restraints: 17286 Sorted by residual: bond pdb=" CA SER B 304 " pdb=" CB SER B 304 " ideal model delta sigma weight residual 1.530 1.461 0.069 1.56e-02 4.11e+03 1.94e+01 bond pdb=" CA SER E 304 " pdb=" CB SER E 304 " ideal model delta sigma weight residual 1.530 1.461 0.069 1.56e-02 4.11e+03 1.94e+01 bond pdb=" CA SER B 152 " pdb=" CB SER B 152 " ideal model delta sigma weight residual 1.536 1.469 0.068 1.58e-02 4.01e+03 1.83e+01 bond pdb=" CA SER E 152 " pdb=" CB SER E 152 " ideal model delta sigma weight residual 1.536 1.469 0.068 1.58e-02 4.01e+03 1.83e+01 bond pdb=" CE1 HIS D 139 " pdb=" NE2 HIS D 139 " ideal model delta sigma weight residual 1.321 1.363 -0.042 1.00e-02 1.00e+04 1.78e+01 ... (remaining 17281 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 19584 2.05 - 4.11: 3554 4.11 - 6.16: 382 6.16 - 8.21: 54 8.21 - 10.27: 18 Bond angle restraints: 23592 Sorted by residual: angle pdb=" CA THR B 236 " pdb=" CB THR B 236 " pdb=" OG1 THR B 236 " ideal model delta sigma weight residual 109.60 99.33 10.27 1.50e+00 4.44e-01 4.68e+01 angle pdb=" CA THR E 236 " pdb=" CB THR E 236 " pdb=" OG1 THR E 236 " ideal model delta sigma weight residual 109.60 99.33 10.27 1.50e+00 4.44e-01 4.68e+01 angle pdb=" CA THR C 236 " pdb=" CB THR C 236 " pdb=" OG1 THR C 236 " ideal model delta sigma weight residual 109.60 100.18 9.42 1.50e+00 4.44e-01 3.94e+01 angle pdb=" CA THR F 236 " pdb=" CB THR F 236 " pdb=" OG1 THR F 236 " ideal model delta sigma weight residual 109.60 100.18 9.42 1.50e+00 4.44e-01 3.94e+01 angle pdb=" CA THR D 236 " pdb=" CB THR D 236 " pdb=" OG1 THR D 236 " ideal model delta sigma weight residual 109.60 100.48 9.12 1.50e+00 4.44e-01 3.70e+01 ... (remaining 23587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 9482 15.26 - 30.53: 748 30.53 - 45.79: 184 45.79 - 61.05: 110 61.05 - 76.32: 50 Dihedral angle restraints: 10574 sinusoidal: 4682 harmonic: 5892 Sorted by residual: dihedral pdb=" CA ARG F 54 " pdb=" C ARG F 54 " pdb=" N GLN F 55 " pdb=" CA GLN F 55 " ideal model delta harmonic sigma weight residual -180.00 -159.02 -20.98 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA ARG C 54 " pdb=" C ARG C 54 " pdb=" N GLN C 55 " pdb=" CA GLN C 55 " ideal model delta harmonic sigma weight residual -180.00 -159.02 -20.98 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA LYS B 117 " pdb=" C LYS B 117 " pdb=" N PHE B 118 " pdb=" CA PHE B 118 " ideal model delta harmonic sigma weight residual 180.00 -163.22 -16.78 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 10571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1660 0.082 - 0.164: 764 0.164 - 0.246: 260 0.246 - 0.328: 38 0.328 - 0.410: 2 Chirality restraints: 2724 Sorted by residual: chirality pdb=" C3' U G 24 " pdb=" C4' U G 24 " pdb=" O3' U G 24 " pdb=" C2' U G 24 " both_signs ideal model delta sigma weight residual False -2.48 -2.89 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" C3' U R 24 " pdb=" C4' U R 24 " pdb=" O3' U R 24 " pdb=" C2' U R 24 " both_signs ideal model delta sigma weight residual False -2.48 -2.89 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" P U R 1 " pdb=" OP1 U R 1 " pdb=" OP2 U R 1 " pdb=" O5' U R 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.72 -0.31 2.00e-01 2.50e+01 2.38e+00 ... (remaining 2721 not shown) Planarity restraints: 2850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 341 " -0.531 9.50e-02 1.11e+02 2.38e-01 3.68e+01 pdb=" NE ARG F 341 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG F 341 " 0.031 2.00e-02 2.50e+03 pdb=" NH1 ARG F 341 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG F 341 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 341 " 0.531 9.50e-02 1.11e+02 2.38e-01 3.68e+01 pdb=" NE ARG C 341 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG C 341 " -0.031 2.00e-02 2.50e+03 pdb=" NH1 ARG C 341 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 341 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 263 " -0.431 9.50e-02 1.11e+02 1.93e-01 2.33e+01 pdb=" NE ARG B 263 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG B 263 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 263 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 263 " -0.011 2.00e-02 2.50e+03 ... (remaining 2847 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 6666 2.91 - 3.40: 17176 3.40 - 3.90: 28312 3.90 - 4.40: 32622 4.40 - 4.90: 51616 Nonbonded interactions: 136392 Sorted by model distance: nonbonded pdb=" O ALA F 251 " pdb=" OG1 THR F 254 " model vdw 2.406 3.040 nonbonded pdb=" O ALA C 251 " pdb=" OG1 THR C 254 " model vdw 2.406 3.040 nonbonded pdb=" OD1 ASP E 250 " pdb=" OG1 THR E 252 " model vdw 2.417 3.040 nonbonded pdb=" OD1 ASP B 250 " pdb=" OG1 THR B 252 " model vdw 2.417 3.040 nonbonded pdb=" OG1 THR C 37 " pdb=" O LEU D 128 " model vdw 2.430 3.040 ... (remaining 136387 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'R' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.16 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: 0.190 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: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.350 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 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 : 0.011 0.069 17286 Z= 0.703 Angle : 1.599 10.267 23592 Z= 1.096 Chirality : 0.100 0.410 2724 Planarity : 0.017 0.238 2850 Dihedral : 14.162 76.317 6774 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.12 % Allowed : 8.02 % Favored : 91.86 % 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: -1.85 (0.16), residues: 2020 helix: -0.99 (0.13), residues: 1140 sheet: None (None), residues: 0 loop : -1.40 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.004 ARG F 341 TYR 0.054 0.010 TYR B 339 PHE 0.050 0.009 PHE C 118 TRP 0.053 0.015 TRP B 196 HIS 0.018 0.005 HIS E 92 Details of bonding type rmsd/Z covalent geometry : bond 0.01113 / 0.70 (17286) covalent geometry : angle 1.59867 / 1.10 (23592) hydrogen bonds : bond 0.19895 / 13.55 ( 840) hydrogen bonds : angle 7.08817 / 5.16 ( 2322) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 207 time to evaluate : 0.661 Fit side-chains REVERT: A 126 ARG cc_start: 0.8533 (ptm160) cc_final: 0.7422 (ptp-170) REVERT: A 352 GLU cc_start: 0.9337 (tt0) cc_final: 0.8980 (pm20) REVERT: B 235 MET cc_start: 0.9107 (mtp) cc_final: 0.8900 (ttm) REVERT: B 244 TYR cc_start: 0.9018 (t80) cc_final: 0.8539 (t80) REVERT: B 352 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8383 (mp0) REVERT: C 186 GLN cc_start: 0.9478 (tt0) cc_final: 0.9231 (tm-30) REVERT: D 126 ARG cc_start: 0.8533 (ptm160) cc_final: 0.7464 (ptp-170) REVERT: D 352 GLU cc_start: 0.9351 (tt0) cc_final: 0.9080 (pm20) REVERT: E 160 GLU cc_start: 0.9329 (mm-30) cc_final: 0.9121 (tp30) REVERT: E 244 TYR cc_start: 0.8988 (t80) cc_final: 0.8521 (t80) REVERT: E 352 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8324 (mp0) REVERT: F 186 GLN cc_start: 0.9444 (tt0) cc_final: 0.9037 (tm-30) outliers start: 2 outliers final: 2 residues processed: 209 average time/residue: 0.1476 time to fit residues: 43.3627 Evaluate side-chains 127 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain E residue 113 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 GLN ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 GLN B 178 HIS C 200 GLN C 301 ASN C 314 ASN D 63 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN E 178 HIS ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 200 GLN F 301 ASN F 314 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.083395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.063976 restraints weight = 41320.387| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.38 r_work: 0.2788 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17286 Z= 0.130 Angle : 0.540 7.007 23592 Z= 0.281 Chirality : 0.038 0.130 2724 Planarity : 0.004 0.041 2850 Dihedral : 10.144 59.937 2958 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.93 % Allowed : 9.59 % Favored : 89.48 % 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: 0.87 (0.18), residues: 2020 helix: 1.41 (0.15), residues: 1162 sheet: None (None), residues: 0 loop : -0.54 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 340 TYR 0.017 0.002 TYR C 308 PHE 0.008 0.001 PHE D 206 TRP 0.010 0.002 TRP C 309 HIS 0.004 0.001 HIS D 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (17286) covalent geometry : angle 0.53967 / 0.28 (23592) hydrogen bonds : bond 0.05047 / 3.45 ( 840) hydrogen bonds : angle 4.45459 / 3.23 ( 2322) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 126 ARG cc_start: 0.8032 (ptm160) cc_final: 0.7156 (ptp-170) REVERT: B 189 ASN cc_start: 0.8588 (m-40) cc_final: 0.8098 (t0) REVERT: B 352 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8008 (mp0) REVERT: C 321 ARG cc_start: 0.8829 (mtp85) cc_final: 0.8613 (mtp85) REVERT: D 126 ARG cc_start: 0.8025 (ptm160) cc_final: 0.7260 (ptp-170) REVERT: E 170 MET cc_start: 0.8769 (mmm) cc_final: 0.8418 (mmm) REVERT: E 189 ASN cc_start: 0.8790 (m-40) cc_final: 0.8271 (t0) REVERT: E 235 MET cc_start: 0.8674 (mtm) cc_final: 0.8454 (mtp) REVERT: F 321 ARG cc_start: 0.8880 (mtp85) cc_final: 0.8650 (mtp85) outliers start: 16 outliers final: 6 residues processed: 154 average time/residue: 0.1276 time to fit residues: 29.4654 Evaluate side-chains 129 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 123 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain E residue 61 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 128 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 139 optimal weight: 20.0000 chunk 150 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 180 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.079468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.059844 restraints weight = 42263.109| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 3.49 r_work: 0.2693 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 17286 Z= 0.198 Angle : 0.553 7.389 23592 Z= 0.285 Chirality : 0.040 0.138 2724 Planarity : 0.004 0.036 2850 Dihedral : 10.150 60.113 2956 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.22 % Allowed : 10.12 % Favored : 88.66 % 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: 1.27 (0.19), residues: 2020 helix: 1.67 (0.15), residues: 1162 sheet: None (None), residues: 0 loop : -0.26 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 321 TYR 0.015 0.002 TYR A 244 PHE 0.010 0.001 PHE E 282 TRP 0.007 0.001 TRP F 309 HIS 0.004 0.001 HIS E 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (17286) covalent geometry : angle 0.55282 / 0.28 (23592) hydrogen bonds : bond 0.05369 / 3.69 ( 840) hydrogen bonds : angle 4.37313 / 3.16 ( 2322) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.486 Fit side-chains REVERT: A 126 ARG cc_start: 0.7986 (ptm160) cc_final: 0.7094 (ptp-170) REVERT: B 170 MET cc_start: 0.8692 (mmm) cc_final: 0.8099 (mmp) REVERT: B 189 ASN cc_start: 0.8853 (m-40) cc_final: 0.8336 (t0) REVERT: C 321 ARG cc_start: 0.8940 (mtp85) cc_final: 0.8677 (mtp85) REVERT: D 126 ARG cc_start: 0.8013 (ptm160) cc_final: 0.7136 (ptp-170) REVERT: E 189 ASN cc_start: 0.8854 (m-40) cc_final: 0.8317 (t0) REVERT: F 321 ARG cc_start: 0.8922 (mtp85) cc_final: 0.8677 (mtp85) outliers start: 21 outliers final: 16 residues processed: 145 average time/residue: 0.1275 time to fit residues: 28.4511 Evaluate side-chains 124 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 363 MET Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 123 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 127 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 173 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 GLN D 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.081322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.061567 restraints weight = 41466.988| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 3.47 r_work: 0.2737 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17286 Z= 0.124 Angle : 0.488 8.128 23592 Z= 0.248 Chirality : 0.038 0.135 2724 Planarity : 0.003 0.036 2850 Dihedral : 10.050 60.068 2956 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.34 % Allowed : 11.28 % Favored : 87.38 % 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: 1.61 (0.19), residues: 2020 helix: 1.91 (0.16), residues: 1162 sheet: None (None), residues: 0 loop : -0.05 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 321 TYR 0.013 0.001 TYR D 100 PHE 0.008 0.001 PHE A 90 TRP 0.010 0.001 TRP F 309 HIS 0.003 0.001 HIS D 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (17286) covalent geometry : angle 0.48781 / 0.25 (23592) hydrogen bonds : bond 0.04197 / 2.88 ( 840) hydrogen bonds : angle 4.03355 / 2.91 ( 2322) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.605 Fit side-chains REVERT: A 126 ARG cc_start: 0.8002 (ptm160) cc_final: 0.7158 (ptm160) REVERT: B 189 ASN cc_start: 0.8862 (m-40) cc_final: 0.8308 (t0) REVERT: C 321 ARG cc_start: 0.8950 (mtp85) cc_final: 0.8736 (mtp85) REVERT: D 126 ARG cc_start: 0.8036 (ptm160) cc_final: 0.7221 (ptm160) REVERT: E 170 MET cc_start: 0.8657 (mmm) cc_final: 0.7960 (mmm) REVERT: E 189 ASN cc_start: 0.8862 (m-40) cc_final: 0.8289 (t0) REVERT: F 321 ARG cc_start: 0.8953 (mtp85) cc_final: 0.8736 (mtp85) outliers start: 23 outliers final: 13 residues processed: 137 average time/residue: 0.1174 time to fit residues: 25.0812 Evaluate side-chains 124 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 124 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 162 optimal weight: 2.9990 chunk 184 optimal weight: 0.7980 chunk 15 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 190 optimal weight: 1.9990 chunk 203 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 101 optimal weight: 30.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.082736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.063167 restraints weight = 41130.366| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.44 r_work: 0.2774 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17286 Z= 0.097 Angle : 0.475 8.467 23592 Z= 0.238 Chirality : 0.037 0.138 2724 Planarity : 0.003 0.032 2850 Dihedral : 9.975 60.067 2956 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.63 % Allowed : 11.51 % Favored : 86.86 % 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: 1.75 (0.19), residues: 2020 helix: 2.02 (0.16), residues: 1162 sheet: None (None), residues: 0 loop : 0.02 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 321 TYR 0.011 0.001 TYR A 244 PHE 0.007 0.001 PHE D 90 TRP 0.009 0.001 TRP C 309 HIS 0.002 0.000 HIS D 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (17286) covalent geometry : angle 0.47463 / 0.24 (23592) hydrogen bonds : bond 0.03663 / 2.52 ( 840) hydrogen bonds : angle 3.88531 / 2.80 ( 2322) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 0.525 Fit side-chains REVERT: A 68 MET cc_start: 0.9137 (mtt) cc_final: 0.8628 (ptp) REVERT: A 123 THR cc_start: 0.7316 (OUTLIER) cc_final: 0.7035 (m) REVERT: A 126 ARG cc_start: 0.7992 (ptm160) cc_final: 0.7192 (ptm160) REVERT: B 189 ASN cc_start: 0.8878 (m-40) cc_final: 0.8285 (t0) REVERT: C 321 ARG cc_start: 0.8958 (mtp85) cc_final: 0.8758 (mtp85) REVERT: D 126 ARG cc_start: 0.8056 (ptm160) cc_final: 0.7305 (ptm160) REVERT: E 189 ASN cc_start: 0.8908 (m-40) cc_final: 0.8320 (t0) REVERT: E 321 ARG cc_start: 0.8798 (mmm-85) cc_final: 0.8364 (mmp80) REVERT: F 321 ARG cc_start: 0.8959 (mtp85) cc_final: 0.8748 (mtp85) outliers start: 28 outliers final: 23 residues processed: 142 average time/residue: 0.1187 time to fit residues: 25.8760 Evaluate side-chains 135 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 124 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 93 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 142 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 102 optimal weight: 30.0000 chunk 193 optimal weight: 2.9990 chunk 196 optimal weight: 0.5980 chunk 44 optimal weight: 8.9990 chunk 147 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.080419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.060837 restraints weight = 41883.915| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.46 r_work: 0.2718 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17286 Z= 0.149 Angle : 0.501 6.625 23592 Z= 0.252 Chirality : 0.038 0.142 2724 Planarity : 0.003 0.034 2850 Dihedral : 9.952 59.986 2956 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.92 % Allowed : 11.74 % 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: 1.68 (0.19), residues: 2020 helix: 1.95 (0.15), residues: 1164 sheet: None (None), residues: 0 loop : 0.01 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 321 TYR 0.013 0.001 TYR A 100 PHE 0.007 0.001 PHE E 282 TRP 0.006 0.001 TRP C 309 HIS 0.003 0.001 HIS E 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (17286) covalent geometry : angle 0.50082 / 0.25 (23592) hydrogen bonds : bond 0.04279 / 2.94 ( 840) hydrogen bonds : angle 3.98754 / 2.88 ( 2322) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.674 Fit side-chains REVERT: B 189 ASN cc_start: 0.8904 (m-40) cc_final: 0.8276 (t0) REVERT: C 321 ARG cc_start: 0.8973 (mtp85) cc_final: 0.8763 (mtp85) REVERT: D 126 ARG cc_start: 0.7985 (ptm160) cc_final: 0.7178 (ptm160) REVERT: E 189 ASN cc_start: 0.8889 (m-40) cc_final: 0.8331 (t0) REVERT: E 321 ARG cc_start: 0.8779 (mmm-85) cc_final: 0.8335 (mmp80) REVERT: F 321 ARG cc_start: 0.8961 (mtp85) cc_final: 0.8748 (mtp85) outliers start: 33 outliers final: 25 residues processed: 139 average time/residue: 0.1240 time to fit residues: 26.9236 Evaluate side-chains 140 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 124 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 89 optimal weight: 10.0000 chunk 166 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 135 optimal weight: 3.9990 chunk 181 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 69 optimal weight: 8.9990 chunk 65 optimal weight: 40.0000 chunk 204 optimal weight: 30.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.079230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.059968 restraints weight = 41462.941| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.39 r_work: 0.2708 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17286 Z= 0.164 Angle : 0.523 11.150 23592 Z= 0.260 Chirality : 0.039 0.147 2724 Planarity : 0.003 0.035 2850 Dihedral : 9.953 59.967 2956 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.15 % Allowed : 11.86 % Favored : 85.99 % 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: 1.61 (0.19), residues: 2020 helix: 1.90 (0.15), residues: 1164 sheet: None (None), residues: 0 loop : -0.03 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 321 TYR 0.013 0.001 TYR D 244 PHE 0.008 0.001 PHE E 282 TRP 0.005 0.001 TRP F 309 HIS 0.003 0.001 HIS B 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (17286) covalent geometry : angle 0.52341 / 0.26 (23592) hydrogen bonds : bond 0.04409 / 3.02 ( 840) hydrogen bonds : angle 4.05447 / 2.93 ( 2322) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: A 63 GLN cc_start: 0.8085 (tp40) cc_final: 0.7809 (tp-100) REVERT: A 68 MET cc_start: 0.9217 (mtt) cc_final: 0.8790 (ptp) REVERT: B 189 ASN cc_start: 0.8899 (m-40) cc_final: 0.8346 (t0) REVERT: C 321 ARG cc_start: 0.8927 (mtp85) cc_final: 0.8698 (mtp85) REVERT: D 126 ARG cc_start: 0.7991 (ptm160) cc_final: 0.7145 (ptm160) REVERT: E 189 ASN cc_start: 0.8893 (m-40) cc_final: 0.8338 (t0) REVERT: E 321 ARG cc_start: 0.8777 (mmm-85) cc_final: 0.8322 (mmp80) REVERT: F 321 ARG cc_start: 0.8920 (mtp85) cc_final: 0.8687 (mtp85) outliers start: 37 outliers final: 27 residues processed: 147 average time/residue: 0.1325 time to fit residues: 30.5094 Evaluate side-chains 140 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 124 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 200 optimal weight: 5.9990 chunk 202 optimal weight: 20.0000 chunk 61 optimal weight: 8.9990 chunk 134 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 74 optimal weight: 30.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.079354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.060095 restraints weight = 41798.253| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 3.42 r_work: 0.2708 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17286 Z= 0.154 Angle : 0.525 11.309 23592 Z= 0.259 Chirality : 0.038 0.148 2724 Planarity : 0.003 0.036 2850 Dihedral : 9.945 59.967 2956 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.92 % Allowed : 12.09 % Favored : 85.99 % 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: 1.63 (0.19), residues: 2020 helix: 1.90 (0.15), residues: 1164 sheet: None (None), residues: 0 loop : -0.00 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 321 TYR 0.012 0.001 TYR D 244 PHE 0.007 0.001 PHE B 282 TRP 0.007 0.001 TRP F 309 HIS 0.003 0.001 HIS B 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (17286) covalent geometry : angle 0.52511 / 0.26 (23592) hydrogen bonds : bond 0.04318 / 2.96 ( 840) hydrogen bonds : angle 4.01940 / 2.91 ( 2322) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.617 Fit side-chains REVERT: A 186 GLN cc_start: 0.9400 (tt0) cc_final: 0.8975 (pp30) REVERT: B 189 ASN cc_start: 0.8902 (m-40) cc_final: 0.8326 (t0) REVERT: C 119 TYR cc_start: 0.8635 (p90) cc_final: 0.8360 (p90) REVERT: C 321 ARG cc_start: 0.8935 (mtp85) cc_final: 0.8688 (mmm-85) REVERT: D 68 MET cc_start: 0.9140 (mtt) cc_final: 0.8655 (ptp) REVERT: D 126 ARG cc_start: 0.7994 (ptm160) cc_final: 0.7159 (ptm160) REVERT: D 186 GLN cc_start: 0.9399 (tt0) cc_final: 0.8982 (pp30) REVERT: E 170 MET cc_start: 0.8607 (mmm) cc_final: 0.8356 (mmt) REVERT: E 189 ASN cc_start: 0.8891 (m-40) cc_final: 0.8319 (t0) REVERT: E 321 ARG cc_start: 0.8766 (mmm-85) cc_final: 0.8316 (mmp80) REVERT: F 321 ARG cc_start: 0.8919 (mtp85) cc_final: 0.8671 (mmm-85) outliers start: 33 outliers final: 27 residues processed: 144 average time/residue: 0.1187 time to fit residues: 26.6911 Evaluate side-chains 141 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 124 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 130 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 9 optimal weight: 30.0000 chunk 90 optimal weight: 3.9990 chunk 191 optimal weight: 0.3980 chunk 15 optimal weight: 5.9990 chunk 25 optimal weight: 0.3980 chunk 62 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 113 optimal weight: 10.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.080838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.061564 restraints weight = 41313.877| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.42 r_work: 0.2743 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17286 Z= 0.113 Angle : 0.510 10.618 23592 Z= 0.249 Chirality : 0.037 0.145 2724 Planarity : 0.003 0.033 2850 Dihedral : 9.918 59.964 2956 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.40 % Allowed : 12.62 % Favored : 85.99 % 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: 1.75 (0.19), residues: 2020 helix: 2.00 (0.15), residues: 1162 sheet: None (None), residues: 0 loop : 0.04 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 321 TYR 0.011 0.001 TYR D 244 PHE 0.006 0.001 PHE D 90 TRP 0.009 0.001 TRP C 309 HIS 0.003 0.000 HIS D 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (17286) covalent geometry : angle 0.50955 / 0.25 (23592) hydrogen bonds : bond 0.03817 / 2.62 ( 840) hydrogen bonds : angle 3.90149 / 2.82 ( 2322) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.655 Fit side-chains REVERT: A 68 MET cc_start: 0.9275 (mtt) cc_final: 0.8952 (ptp) REVERT: A 186 GLN cc_start: 0.9387 (tt0) cc_final: 0.8949 (pp30) REVERT: B 170 MET cc_start: 0.8582 (mmm) cc_final: 0.8331 (mmt) REVERT: B 189 ASN cc_start: 0.8910 (m-40) cc_final: 0.8264 (t0) REVERT: C 321 ARG cc_start: 0.8929 (mtp85) cc_final: 0.8694 (mmm-85) REVERT: D 68 MET cc_start: 0.9153 (mtt) cc_final: 0.8736 (ptp) REVERT: D 126 ARG cc_start: 0.8013 (ptm160) cc_final: 0.7187 (ptm160) REVERT: D 186 GLN cc_start: 0.9371 (tt0) cc_final: 0.8936 (pp30) REVERT: E 189 ASN cc_start: 0.8921 (m-40) cc_final: 0.8257 (t0) REVERT: E 321 ARG cc_start: 0.8761 (mmm-85) cc_final: 0.8317 (mmp80) REVERT: F 321 ARG cc_start: 0.8924 (mtp85) cc_final: 0.8686 (mmm-85) outliers start: 24 outliers final: 22 residues processed: 136 average time/residue: 0.1315 time to fit residues: 27.7057 Evaluate side-chains 134 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 124 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 13 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 9 optimal weight: 30.0000 chunk 58 optimal weight: 4.9990 chunk 65 optimal weight: 20.0000 chunk 135 optimal weight: 20.0000 chunk 175 optimal weight: 4.9990 chunk 196 optimal weight: 0.0050 chunk 8 optimal weight: 30.0000 overall best weight: 4.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.079961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.060733 restraints weight = 41410.274| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 3.41 r_work: 0.2725 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17286 Z= 0.138 Angle : 0.532 10.329 23592 Z= 0.260 Chirality : 0.038 0.146 2724 Planarity : 0.003 0.034 2850 Dihedral : 9.914 59.962 2956 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.34 % Allowed : 12.67 % Favored : 85.99 % 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: 1.71 (0.19), residues: 2020 helix: 1.96 (0.15), residues: 1164 sheet: None (None), residues: 0 loop : 0.04 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 321 TYR 0.012 0.001 TYR D 244 PHE 0.006 0.001 PHE A 90 TRP 0.007 0.001 TRP F 309 HIS 0.003 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (17286) covalent geometry : angle 0.53239 / 0.26 (23592) hydrogen bonds : bond 0.04075 / 2.80 ( 840) hydrogen bonds : angle 3.94530 / 2.86 ( 2322) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.602 Fit side-chains REVERT: A 68 MET cc_start: 0.9190 (mtt) cc_final: 0.8814 (ptp) REVERT: A 186 GLN cc_start: 0.9384 (tt0) cc_final: 0.8986 (pp30) REVERT: B 189 ASN cc_start: 0.8909 (m-40) cc_final: 0.8255 (t0) REVERT: C 321 ARG cc_start: 0.8934 (mtp85) cc_final: 0.8707 (mmm-85) REVERT: D 68 MET cc_start: 0.9152 (mtt) cc_final: 0.8729 (ptp) REVERT: D 126 ARG cc_start: 0.8006 (ptm160) cc_final: 0.7170 (ptm160) REVERT: D 186 GLN cc_start: 0.9374 (tt0) cc_final: 0.9010 (pp30) REVERT: E 189 ASN cc_start: 0.8911 (m-40) cc_final: 0.8267 (t0) REVERT: E 321 ARG cc_start: 0.8759 (mmm-85) cc_final: 0.8316 (mmp80) REVERT: F 321 ARG cc_start: 0.8925 (mtp85) cc_final: 0.8683 (mmm-85) outliers start: 23 outliers final: 23 residues processed: 135 average time/residue: 0.1215 time to fit residues: 25.5187 Evaluate side-chains 135 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 124 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 146 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 chunk 168 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.078608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.059387 restraints weight = 41420.962| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 3.40 r_work: 0.2697 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17286 Z= 0.181 Angle : 0.554 9.975 23592 Z= 0.273 Chirality : 0.039 0.148 2724 Planarity : 0.003 0.036 2850 Dihedral : 9.939 59.937 2956 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.63 % Allowed : 12.38 % Favored : 85.99 % 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: 1.60 (0.19), residues: 2020 helix: 1.87 (0.15), residues: 1162 sheet: None (None), residues: 0 loop : 0.00 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 321 TYR 0.013 0.001 TYR D 244 PHE 0.008 0.001 PHE E 282 TRP 0.005 0.001 TRP C 309 HIS 0.004 0.001 HIS E 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (17286) covalent geometry : angle 0.55422 / 0.27 (23592) hydrogen bonds : bond 0.04543 / 3.12 ( 840) hydrogen bonds : angle 4.07490 / 2.95 ( 2322) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2978.68 seconds wall clock time: 52 minutes 6.02 seconds (3126.02 seconds total)