Starting phenix.real_space_refine on Sat Aug 23 06:27:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wbh_37425/08_2025/8wbh_37425.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wbh_37425/08_2025/8wbh_37425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wbh_37425/08_2025/8wbh_37425.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wbh_37425/08_2025/8wbh_37425.map" model { file = "/net/cci-nas-00/data/ceres_data/8wbh_37425/08_2025/8wbh_37425.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wbh_37425/08_2025/8wbh_37425.cif" } resolution = 3.2 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= -0.000 sd= 0.036 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: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 6415 2.51 5 N 1844 2.21 5 O 1957 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10284 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2652 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 317} Chain breaks: 1 Chain: "B" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2482 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "a" Number of atoms: 2634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2634 Classifications: {'peptide': 331} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 315} Chain breaks: 1 Chain: "b" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2516 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 300} Chain breaks: 1 Time building chain proxies: 3.03, per 1000 atoms: 0.29 Number of scatterers: 10284 At special positions: 0 Unit cell: (90.95, 107.95, 111.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 1957 8.00 N 1844 7.00 C 6415 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 15 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 316 " distance=2.02 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 15 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 312 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 316 " distance=2.03 Simple disulfide: pdb=" SG CYS a 4 " - pdb=" SG CYS a 15 " distance=2.03 Simple disulfide: pdb=" SG CYS a 55 " - pdb=" SG CYS a 143 " distance=2.04 Simple disulfide: pdb=" SG CYS a 179 " - pdb=" SG CYS a 223 " distance=2.03 Simple disulfide: pdb=" SG CYS a 280 " - pdb=" SG CYS a 329 " distance=2.02 Simple disulfide: pdb=" SG CYS a 291 " - pdb=" SG CYS a 312 " distance=2.03 Simple disulfide: pdb=" SG CYS a 313 " - pdb=" SG CYS a 316 " distance=2.03 Simple disulfide: pdb=" SG CYS b 4 " - pdb=" SG CYS b 15 " distance=2.03 Simple disulfide: pdb=" SG CYS b 55 " - pdb=" SG CYS b 143 " distance=2.03 Simple disulfide: pdb=" SG CYS b 179 " - pdb=" SG CYS b 223 " distance=2.03 Simple disulfide: pdb=" SG CYS b 280 " - pdb=" SG CYS b 329 " distance=2.03 Simple disulfide: pdb=" SG CYS b 291 " - pdb=" SG CYS b 312 " distance=2.03 Simple disulfide: pdb=" SG CYS b 313 " - pdb=" SG CYS b 316 " distance=2.03 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: 1.16 Conformation dependent library (CDL) restraints added in 439.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2386 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 20 sheets defined 15.5% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 38 through 53 removed outlier: 3.794A pdb=" N LYS A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 82 removed outlier: 4.736A pdb=" N ASP A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N GLU A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.525A pdb=" N HIS A 229 " --> pdb=" O PRO A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 removed outlier: 3.921A pdb=" N ALA A 248 " --> pdb=" O HIS A 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 53 removed outlier: 3.726A pdb=" N LEU B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS B 44 " --> pdb=" O ARG B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 79 removed outlier: 4.949A pdb=" N ASP B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLU B 74 " --> pdb=" O ALA B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 148 Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.791A pdb=" N THR B 230 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'a' and resid 38 through 53 removed outlier: 3.810A pdb=" N LYS a 44 " --> pdb=" O ARG a 40 " (cutoff:3.500A) Processing helix chain 'a' and resid 61 through 82 removed outlier: 4.909A pdb=" N ASP a 73 " --> pdb=" O GLU a 69 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N GLU a 74 " --> pdb=" O ALA a 70 " (cutoff:3.500A) Processing helix chain 'a' and resid 144 through 146 No H-bonds generated for 'chain 'a' and resid 144 through 146' Processing helix chain 'a' and resid 226 through 230 Processing helix chain 'a' and resid 244 through 248 removed outlier: 3.913A pdb=" N ALA a 248 " --> pdb=" O HIS a 245 " (cutoff:3.500A) Processing helix chain 'b' and resid 38 through 53 removed outlier: 3.609A pdb=" N ALA b 43 " --> pdb=" O PRO b 39 " (cutoff:3.500A) Processing helix chain 'b' and resid 61 through 83 removed outlier: 4.636A pdb=" N ASP b 73 " --> pdb=" O GLU b 69 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLU b 74 " --> pdb=" O ALA b 70 " (cutoff:3.500A) Processing helix chain 'b' and resid 226 through 230 removed outlier: 3.553A pdb=" N THR b 230 " --> pdb=" O GLU b 227 " (cutoff:3.500A) Processing helix chain 'b' and resid 237 through 241 removed outlier: 3.826A pdb=" N LEU b 241 " --> pdb=" O GLU b 238 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 22 Processing sheet with id=AA3, first strand: chain 'A' and resid 32 through 35 removed outlier: 6.311A pdb=" N ARG A 166 " --> pdb=" O PHE A 158 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N PHE A 158 " --> pdb=" O ARG A 166 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TRP A 168 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 90 removed outlier: 6.913A pdb=" N SER A 87 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL A 135 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL A 89 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLY A 56 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 321 through 323 removed outlier: 4.579A pdb=" N PHE A 277 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N GLU A 213 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLU A 203 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA A 215 " --> pdb=" O TRP A 201 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TRP A 201 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL A 192 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL a 192 " --> pdb=" O LYS a 189 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ARG a 205 " --> pdb=" O LEU a 212 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LEU a 212 " --> pdb=" O ARG a 205 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 285 through 286 removed outlier: 6.101A pdb=" N THR A 286 " --> pdb=" O CYS A 313 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 2 through 5 removed outlier: 3.681A pdb=" N THR B 2 " --> pdb=" O ILE b 6 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 32 through 34 removed outlier: 4.714A pdb=" N ASP B 157 " --> pdb=" O TRP B 168 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS B 170 " --> pdb=" O ILE B 155 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ILE B 155 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 57 through 58 Processing sheet with id=AB1, first strand: chain 'B' and resid 321 through 323 removed outlier: 4.194A pdb=" N PHE B 277 " --> pdb=" O GLU B 213 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N GLU B 213 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LEU B 212 " --> pdb=" O ARG B 205 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG B 205 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG B 214 " --> pdb=" O GLU B 203 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL b 192 " --> pdb=" O LYS b 189 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ARG b 205 " --> pdb=" O LEU b 212 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LEU b 212 " --> pdb=" O ARG b 205 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 286 through 287 removed outlier: 7.317A pdb=" N THR B 286 " --> pdb=" O CYS B 313 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'a' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'a' and resid 32 through 35 removed outlier: 6.608A pdb=" N ARG a 166 " --> pdb=" O PHE a 158 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE a 158 " --> pdb=" O ARG a 166 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TRP a 168 " --> pdb=" O GLU a 156 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'a' and resid 56 through 57 removed outlier: 7.292A pdb=" N GLY a 56 " --> pdb=" O ALA a 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'a' and resid 88 through 89 Processing sheet with id=AB7, first strand: chain 'a' and resid 285 through 287 removed outlier: 3.748A pdb=" N CYS a 313 " --> pdb=" O THR a 286 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 32 through 36 removed outlier: 3.517A pdb=" N LYS b 33 " --> pdb=" O THR b 165 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP b 157 " --> pdb=" O TRP b 168 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LYS b 170 " --> pdb=" O ILE b 155 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ILE b 155 " --> pdb=" O LYS b 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 57 through 58 Processing sheet with id=AC1, first strand: chain 'b' and resid 86 through 89 removed outlier: 6.962A pdb=" N SER b 87 " --> pdb=" O PHE b 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'b' and resid 311 through 313 259 hydrogen bonds defined for protein. 699 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.58 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3454 1.34 - 1.47: 2474 1.47 - 1.59: 4510 1.59 - 1.72: 0 1.72 - 1.84: 88 Bond restraints: 10526 Sorted by residual: bond pdb=" C ARG B 336 " pdb=" N PRO B 337 " ideal model delta sigma weight residual 1.334 1.359 -0.025 1.11e-02 8.12e+03 5.08e+00 bond pdb=" N VAL B 338 " pdb=" CA VAL B 338 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" C PRO B 337 " pdb=" O PRO B 337 " ideal model delta sigma weight residual 1.233 1.216 0.018 1.06e-02 8.90e+03 2.75e+00 bond pdb=" CB CYS B 4 " pdb=" SG CYS B 4 " ideal model delta sigma weight residual 1.808 1.774 0.034 3.30e-02 9.18e+02 1.05e+00 bond pdb=" CB CYS a 4 " pdb=" SG CYS a 4 " ideal model delta sigma weight residual 1.808 1.840 -0.032 3.30e-02 9.18e+02 9.50e-01 ... (remaining 10521 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 13865 1.35 - 2.69: 326 2.69 - 4.04: 61 4.04 - 5.38: 17 5.38 - 6.73: 6 Bond angle restraints: 14275 Sorted by residual: angle pdb=" O ARG B 336 " pdb=" C ARG B 336 " pdb=" N PRO B 337 " ideal model delta sigma weight residual 121.80 118.84 2.96 8.60e-01 1.35e+00 1.18e+01 angle pdb=" N ILE b 183 " pdb=" CA ILE b 183 " pdb=" C ILE b 183 " ideal model delta sigma weight residual 113.20 109.98 3.22 9.60e-01 1.09e+00 1.12e+01 angle pdb=" CA ARG A 339 " pdb=" CB ARG A 339 " pdb=" CG ARG A 339 " ideal model delta sigma weight residual 114.10 120.17 -6.07 2.00e+00 2.50e-01 9.20e+00 angle pdb=" C VAL a 338 " pdb=" N ARG a 339 " pdb=" CA ARG a 339 " ideal model delta sigma weight residual 121.90 118.25 3.65 1.26e+00 6.30e-01 8.37e+00 angle pdb=" CA ARG b 103 " pdb=" CB ARG b 103 " pdb=" CG ARG b 103 " ideal model delta sigma weight residual 114.10 119.19 -5.09 2.00e+00 2.50e-01 6.49e+00 ... (remaining 14270 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 5843 17.34 - 34.68: 430 34.68 - 52.02: 59 52.02 - 69.36: 8 69.36 - 86.69: 5 Dihedral angle restraints: 6345 sinusoidal: 2642 harmonic: 3703 Sorted by residual: dihedral pdb=" CB CYS b 55 " pdb=" SG CYS b 55 " pdb=" SG CYS b 143 " pdb=" CB CYS b 143 " ideal model delta sinusoidal sigma weight residual -86.00 -6.23 -79.77 1 1.00e+01 1.00e-02 7.89e+01 dihedral pdb=" CB CYS a 4 " pdb=" SG CYS a 4 " pdb=" SG CYS a 15 " pdb=" CB CYS a 15 " ideal model delta sinusoidal sigma weight residual -86.00 -43.37 -42.63 1 1.00e+01 1.00e-02 2.54e+01 dihedral pdb=" CA CYS B 4 " pdb=" C CYS B 4 " pdb=" N ALA B 5 " pdb=" CA ALA B 5 " ideal model delta harmonic sigma weight residual -180.00 -159.69 -20.31 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 6342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1058 0.037 - 0.073: 329 0.073 - 0.110: 126 0.110 - 0.147: 29 0.147 - 0.184: 4 Chirality restraints: 1546 Sorted by residual: chirality pdb=" CA VAL B 338 " pdb=" N VAL B 338 " pdb=" C VAL B 338 " pdb=" CB VAL B 338 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.43e-01 chirality pdb=" CB VAL B 71 " pdb=" CA VAL B 71 " pdb=" CG1 VAL B 71 " pdb=" CG2 VAL B 71 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.26e-01 chirality pdb=" CB VAL B 338 " pdb=" CA VAL B 338 " pdb=" CG1 VAL B 338 " pdb=" CG2 VAL B 338 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.15 2.00e-01 2.50e+01 5.97e-01 ... (remaining 1543 not shown) Planarity restraints: 1841 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 318 " -0.028 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO B 319 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 319 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 319 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU b 318 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO b 319 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO b 319 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO b 319 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR a 38 " -0.021 5.00e-02 4.00e+02 3.15e-02 1.59e+00 pdb=" N PRO a 39 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO a 39 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO a 39 " -0.018 5.00e-02 4.00e+02 ... (remaining 1838 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 890 2.74 - 3.28: 9349 3.28 - 3.82: 15447 3.82 - 4.36: 18441 4.36 - 4.90: 32976 Nonbonded interactions: 77103 Sorted by model distance: nonbonded pdb=" OG1 THR a 302 " pdb=" O THR a 344 " model vdw 2.203 3.040 nonbonded pdb=" O GLY a 266 " pdb=" OG SER a 348 " model vdw 2.251 3.040 nonbonded pdb=" OG1 THR b 286 " pdb=" O TRP b 311 " model vdw 2.289 3.040 nonbonded pdb=" OE2 GLU B 26 " pdb=" NH2 ARG B 214 " model vdw 2.301 3.120 nonbonded pdb=" OG1 THR A 302 " pdb=" O THR A 344 " model vdw 2.302 3.040 ... (remaining 77098 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 107 or resid 133 throu \ gh 207 or (resid 208 and (name N or name CA or name C or name O or name CB )) or \ resid 209 through 338)) selection = chain 'B' selection = (chain 'a' and (resid 1 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 107 or resid 133 throu \ gh 207 or (resid 208 and (name N or name CA or name C or name O or name CB )) or \ resid 209 through 338)) selection = (chain 'b' and (resid 1 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 107 or resid 133 throu \ gh 207 or (resid 208 and (name N or name CA or name C or name O or name CB )) or \ resid 209 through 338)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.780 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 11.790 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 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 : 0.003 0.034 10550 Z= 0.116 Angle : 0.542 6.728 14323 Z= 0.288 Chirality : 0.043 0.184 1546 Planarity : 0.003 0.043 1841 Dihedral : 11.714 86.694 3887 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.03 % Favored : 93.81 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -1.76 (0.22), residues: 1277 helix: 1.90 (0.44), residues: 145 sheet: -1.50 (0.37), residues: 223 loop : -1.71 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 14 TYR 0.006 0.001 TYR a 331 PHE 0.009 0.001 PHE a 20 TRP 0.012 0.001 TRP a 330 HIS 0.006 0.001 HIS a 340 Details of bonding type rmsd covalent geometry : bond 0.00254 (10526) covalent geometry : angle 0.53609 (14275) SS BOND : bond 0.00268 ( 24) SS BOND : angle 1.47853 ( 48) hydrogen bonds : bond 0.21277 ( 259) hydrogen bonds : angle 7.93699 ( 699) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8415 (tttm) cc_final: 0.8006 (mttm) REVERT: A 86 LEU cc_start: 0.8118 (tt) cc_final: 0.7874 (tt) REVERT: A 146 GLU cc_start: 0.7997 (pt0) cc_final: 0.7637 (mp0) REVERT: A 197 ASP cc_start: 0.8514 (p0) cc_final: 0.8312 (p0) REVERT: A 261 LYS cc_start: 0.8503 (mttt) cc_final: 0.8290 (mtpt) REVERT: A 293 LYS cc_start: 0.8679 (mmmt) cc_final: 0.8437 (mmtt) REVERT: A 309 THR cc_start: 0.8097 (p) cc_final: 0.7848 (m) REVERT: B 33 LYS cc_start: 0.8074 (tttt) cc_final: 0.7863 (mtmt) REVERT: B 136 ASP cc_start: 0.6893 (t0) cc_final: 0.6542 (p0) REVERT: B 256 ARG cc_start: 0.8193 (ptt90) cc_final: 0.7648 (ptt-90) REVERT: B 298 VAL cc_start: 0.8221 (p) cc_final: 0.8014 (m) REVERT: a 44 LYS cc_start: 0.8467 (tptt) cc_final: 0.8245 (mttm) REVERT: a 72 ARG cc_start: 0.8099 (ttp80) cc_final: 0.7849 (ttp-170) REVERT: b 7 ASP cc_start: 0.7269 (m-30) cc_final: 0.6922 (t0) REVERT: b 207 ASN cc_start: 0.6699 (t0) cc_final: 0.6100 (p0) REVERT: b 265 GLN cc_start: 0.7374 (mt0) cc_final: 0.7037 (mm-40) REVERT: b 314 ARG cc_start: 0.5451 (ttm-80) cc_final: 0.5143 (mtp85) REVERT: b 324 ARG cc_start: 0.7888 (ttt-90) cc_final: 0.6970 (ttm170) REVERT: b 331 TYR cc_start: 0.7357 (m-80) cc_final: 0.7097 (m-10) REVERT: b 337 PRO cc_start: 0.8331 (Cg_endo) cc_final: 0.7912 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.1554 time to fit residues: 48.6491 Evaluate side-chains 143 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.0060 chunk 10 optimal weight: 0.0470 chunk 66 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.1898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 263 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.182940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.126401 restraints weight = 12204.479| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.89 r_work: 0.3336 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10550 Z= 0.147 Angle : 0.644 18.948 14323 Z= 0.336 Chirality : 0.045 0.192 1546 Planarity : 0.005 0.084 1841 Dihedral : 4.454 29.518 1412 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.81 % Favored : 93.03 % Rotamer: Outliers : 2.29 % Allowed : 7.76 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -1.77 (0.23), residues: 1277 helix: 1.98 (0.43), residues: 149 sheet: -1.80 (0.33), residues: 255 loop : -1.63 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 336 TYR 0.007 0.001 TYR a 331 PHE 0.010 0.001 PHE a 217 TRP 0.009 0.001 TRP a 330 HIS 0.005 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00343 (10526) covalent geometry : angle 0.61998 (14275) SS BOND : bond 0.00300 ( 24) SS BOND : angle 3.04434 ( 48) hydrogen bonds : bond 0.04351 ( 259) hydrogen bonds : angle 5.66865 ( 699) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8155 (tttm) cc_final: 0.7576 (mttm) REVERT: A 48 LYS cc_start: 0.8682 (tptp) cc_final: 0.8139 (tttt) REVERT: A 86 LEU cc_start: 0.8132 (tt) cc_final: 0.7890 (tt) REVERT: A 146 GLU cc_start: 0.8202 (pt0) cc_final: 0.7620 (mp0) REVERT: A 261 LYS cc_start: 0.8633 (mttt) cc_final: 0.8353 (mtpt) REVERT: A 293 LYS cc_start: 0.8855 (mmmt) cc_final: 0.8488 (mmtt) REVERT: A 309 THR cc_start: 0.8095 (p) cc_final: 0.7859 (m) REVERT: B 33 LYS cc_start: 0.7385 (tttt) cc_final: 0.7021 (mtmt) REVERT: B 67 MET cc_start: 0.7118 (ttp) cc_final: 0.6891 (ttp) REVERT: B 157 ASP cc_start: 0.7767 (p0) cc_final: 0.7343 (p0) REVERT: B 168 TRP cc_start: 0.7299 (m-10) cc_final: 0.6745 (m100) REVERT: B 256 ARG cc_start: 0.8321 (ptt90) cc_final: 0.7610 (ptt-90) REVERT: B 336 ARG cc_start: 0.4040 (OUTLIER) cc_final: 0.3315 (mmp80) REVERT: a 44 LYS cc_start: 0.8481 (tptt) cc_final: 0.8235 (mttt) REVERT: b 7 ASP cc_start: 0.6906 (m-30) cc_final: 0.6333 (t0) REVERT: b 263 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.7154 (mt0) REVERT: b 265 GLN cc_start: 0.7405 (mt0) cc_final: 0.7057 (mm-40) REVERT: b 289 GLU cc_start: 0.8031 (mp0) cc_final: 0.7665 (pm20) REVERT: b 324 ARG cc_start: 0.8079 (ttt-90) cc_final: 0.7012 (ttm170) REVERT: b 331 TYR cc_start: 0.7295 (m-80) cc_final: 0.7003 (m-10) REVERT: b 337 PRO cc_start: 0.8440 (Cg_endo) cc_final: 0.7996 (Cg_exo) outliers start: 26 outliers final: 17 residues processed: 166 average time/residue: 0.1358 time to fit residues: 29.9231 Evaluate side-chains 153 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain a residue 4 CYS Chi-restraints excluded: chain a residue 15 CYS Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 94 VAL Chi-restraints excluded: chain a residue 176 THR Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 243 ILE Chi-restraints excluded: chain b residue 22 HIS Chi-restraints excluded: chain b residue 227 GLU Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 263 GLN Chi-restraints excluded: chain b residue 334 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 10 optimal weight: 0.0670 chunk 99 optimal weight: 4.9990 chunk 73 optimal weight: 0.2980 chunk 62 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS A 66 GLN B 22 HIS ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN a 207 ASN b 263 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.183793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3615 r_free = 0.3615 target = 0.130483 restraints weight = 12449.356| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.15 r_work: 0.3395 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10550 Z= 0.113 Angle : 0.584 15.873 14323 Z= 0.304 Chirality : 0.043 0.154 1546 Planarity : 0.004 0.071 1841 Dihedral : 4.281 29.634 1412 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.48 % Favored : 94.36 % Rotamer: Outliers : 2.47 % Allowed : 11.90 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -1.63 (0.22), residues: 1277 helix: 2.23 (0.43), residues: 149 sheet: -1.58 (0.35), residues: 230 loop : -1.63 (0.19), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 336 TYR 0.008 0.001 TYR a 206 PHE 0.009 0.001 PHE a 217 TRP 0.007 0.001 TRP a 330 HIS 0.004 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00260 (10526) covalent geometry : angle 0.56738 (14275) SS BOND : bond 0.00220 ( 24) SS BOND : angle 2.47972 ( 48) hydrogen bonds : bond 0.03592 ( 259) hydrogen bonds : angle 5.25843 ( 699) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.8757 (tptp) cc_final: 0.8445 (tttt) REVERT: A 146 GLU cc_start: 0.8189 (pt0) cc_final: 0.7814 (mp0) REVERT: A 309 THR cc_start: 0.8053 (p) cc_final: 0.7835 (m) REVERT: B 67 MET cc_start: 0.7297 (ttp) cc_final: 0.7088 (ttp) REVERT: B 256 ARG cc_start: 0.8118 (ptt90) cc_final: 0.7775 (ptt-90) REVERT: B 336 ARG cc_start: 0.4183 (OUTLIER) cc_final: 0.3247 (mmp80) REVERT: a 208 ASP cc_start: 0.8013 (m-30) cc_final: 0.7782 (m-30) REVERT: b 7 ASP cc_start: 0.7278 (m-30) cc_final: 0.6857 (t0) REVERT: b 289 GLU cc_start: 0.7998 (mp0) cc_final: 0.7693 (pm20) REVERT: b 324 ARG cc_start: 0.7907 (ttt-90) cc_final: 0.7152 (ttm170) REVERT: b 331 TYR cc_start: 0.7545 (m-80) cc_final: 0.7326 (m-10) outliers start: 28 outliers final: 20 residues processed: 161 average time/residue: 0.1335 time to fit residues: 28.5165 Evaluate side-chains 143 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 22 HIS Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain a residue 4 CYS Chi-restraints excluded: chain a residue 15 CYS Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 94 VAL Chi-restraints excluded: chain a residue 176 THR Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 243 ILE Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain b residue 22 HIS Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 175 SER Chi-restraints excluded: chain b residue 227 GLU Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 262 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 43 optimal weight: 0.0870 chunk 85 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS B 22 HIS ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 263 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.179110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.132725 restraints weight = 12582.392| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.01 r_work: 0.3359 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10550 Z= 0.181 Angle : 0.635 16.527 14323 Z= 0.331 Chirality : 0.045 0.163 1546 Planarity : 0.004 0.074 1841 Dihedral : 4.586 28.405 1412 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.44 % Favored : 92.40 % Rotamer: Outliers : 3.53 % Allowed : 13.32 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -1.73 (0.22), residues: 1277 helix: 2.25 (0.42), residues: 149 sheet: -1.82 (0.33), residues: 260 loop : -1.63 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 166 TYR 0.009 0.001 TYR a 206 PHE 0.012 0.002 PHE a 217 TRP 0.010 0.001 TRP A 330 HIS 0.007 0.001 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00438 (10526) covalent geometry : angle 0.61852 (14275) SS BOND : bond 0.00325 ( 24) SS BOND : angle 2.52657 ( 48) hydrogen bonds : bond 0.03927 ( 259) hydrogen bonds : angle 5.22995 ( 699) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 127 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.8810 (tptp) cc_final: 0.8483 (tttt) REVERT: A 146 GLU cc_start: 0.8351 (pt0) cc_final: 0.7833 (mp0) REVERT: A 309 THR cc_start: 0.8190 (p) cc_final: 0.7953 (m) REVERT: B 67 MET cc_start: 0.7372 (ttp) cc_final: 0.7118 (ttp) REVERT: B 324 ARG cc_start: 0.8077 (ttp80) cc_final: 0.7601 (ttm170) REVERT: B 336 ARG cc_start: 0.4367 (OUTLIER) cc_final: 0.3555 (mtp85) REVERT: a 208 ASP cc_start: 0.8185 (m-30) cc_final: 0.7982 (m-30) REVERT: b 7 ASP cc_start: 0.7411 (m-30) cc_final: 0.6841 (t0) REVERT: b 289 GLU cc_start: 0.8025 (mp0) cc_final: 0.7696 (pm20) REVERT: b 324 ARG cc_start: 0.8101 (ttt-90) cc_final: 0.7261 (ttm170) REVERT: b 331 TYR cc_start: 0.7659 (m-80) cc_final: 0.7414 (m-10) outliers start: 40 outliers final: 29 residues processed: 155 average time/residue: 0.1282 time to fit residues: 26.7018 Evaluate side-chains 151 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 HIS Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain B residue 22 HIS Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain a residue 4 CYS Chi-restraints excluded: chain a residue 15 CYS Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain a residue 42 LEU Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 94 VAL Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 176 THR Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 243 ILE Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain b residue 22 HIS Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 227 GLU Chi-restraints excluded: chain b residue 262 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 111 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS B 22 HIS B 147 HIS ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.179252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 110)---------------| | r_work = 0.3531 r_free = 0.3531 target = 0.124435 restraints weight = 12380.973| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.30 r_work: 0.3340 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10550 Z= 0.143 Angle : 0.610 14.994 14323 Z= 0.317 Chirality : 0.044 0.155 1546 Planarity : 0.004 0.051 1841 Dihedral : 4.489 27.596 1412 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.50 % Favored : 93.34 % Rotamer: Outliers : 3.70 % Allowed : 14.90 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -1.67 (0.23), residues: 1277 helix: 2.35 (0.42), residues: 149 sheet: -1.77 (0.34), residues: 245 loop : -1.62 (0.19), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 166 TYR 0.008 0.001 TYR a 206 PHE 0.011 0.001 PHE a 217 TRP 0.007 0.001 TRP A 150 HIS 0.010 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00342 (10526) covalent geometry : angle 0.59479 (14275) SS BOND : bond 0.00236 ( 24) SS BOND : angle 2.44582 ( 48) hydrogen bonds : bond 0.03602 ( 259) hydrogen bonds : angle 5.11185 ( 699) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.8776 (tptp) cc_final: 0.8412 (tttt) REVERT: A 146 GLU cc_start: 0.8357 (pt0) cc_final: 0.7759 (mp0) REVERT: A 309 THR cc_start: 0.8214 (p) cc_final: 0.7940 (m) REVERT: B 67 MET cc_start: 0.7285 (ttp) cc_final: 0.7009 (ttp) REVERT: B 324 ARG cc_start: 0.8108 (ttp80) cc_final: 0.7486 (ttm170) REVERT: B 336 ARG cc_start: 0.4329 (OUTLIER) cc_final: 0.3183 (mmp80) REVERT: b 7 ASP cc_start: 0.7202 (m-30) cc_final: 0.6624 (t0) REVERT: b 289 GLU cc_start: 0.8080 (mp0) cc_final: 0.7646 (pm20) REVERT: b 324 ARG cc_start: 0.8163 (ttt-90) cc_final: 0.7116 (ttm170) outliers start: 42 outliers final: 33 residues processed: 157 average time/residue: 0.1338 time to fit residues: 28.3056 Evaluate side-chains 154 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 HIS Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain a residue 4 CYS Chi-restraints excluded: chain a residue 15 CYS Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain a residue 42 LEU Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 94 VAL Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 176 THR Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 243 ILE Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 273 ILE Chi-restraints excluded: chain a residue 307 LEU Chi-restraints excluded: chain b residue 22 HIS Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 175 SER Chi-restraints excluded: chain b residue 227 GLU Chi-restraints excluded: chain b residue 238 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 70 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 85 optimal weight: 0.0370 chunk 118 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 127 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 overall best weight: 1.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.179457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.140846 restraints weight = 12530.091| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.99 r_work: 0.3360 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10550 Z= 0.151 Angle : 0.616 14.620 14323 Z= 0.320 Chirality : 0.044 0.203 1546 Planarity : 0.004 0.036 1841 Dihedral : 4.480 27.613 1412 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.13 % Favored : 92.72 % Rotamer: Outliers : 4.14 % Allowed : 15.43 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -1.64 (0.23), residues: 1277 helix: 2.40 (0.42), residues: 149 sheet: -1.76 (0.34), residues: 244 loop : -1.61 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 314 TYR 0.008 0.001 TYR b 331 PHE 0.011 0.002 PHE a 217 TRP 0.008 0.001 TRP A 330 HIS 0.009 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00361 (10526) covalent geometry : angle 0.60066 (14275) SS BOND : bond 0.00215 ( 24) SS BOND : angle 2.40856 ( 48) hydrogen bonds : bond 0.03574 ( 259) hydrogen bonds : angle 5.07919 ( 699) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 117 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.8801 (tptp) cc_final: 0.8469 (tttt) REVERT: A 146 GLU cc_start: 0.8360 (pt0) cc_final: 0.7840 (mp0) REVERT: A 309 THR cc_start: 0.8196 (p) cc_final: 0.7945 (m) REVERT: B 67 MET cc_start: 0.7345 (ttp) cc_final: 0.7080 (ttp) REVERT: B 324 ARG cc_start: 0.8113 (ttp80) cc_final: 0.7559 (ttm170) REVERT: B 336 ARG cc_start: 0.4419 (OUTLIER) cc_final: 0.3274 (mmp80) REVERT: b 7 ASP cc_start: 0.7188 (m-30) cc_final: 0.6680 (t0) REVERT: b 263 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7244 (mt0) REVERT: b 289 GLU cc_start: 0.8116 (mp0) cc_final: 0.7672 (pm20) REVERT: b 324 ARG cc_start: 0.8098 (ttt-90) cc_final: 0.7205 (ttm170) outliers start: 47 outliers final: 38 residues processed: 152 average time/residue: 0.1163 time to fit residues: 24.2271 Evaluate side-chains 152 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 112 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 HIS Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain a residue 4 CYS Chi-restraints excluded: chain a residue 15 CYS Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain a residue 42 LEU Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 94 VAL Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 243 ILE Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 307 LEU Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 22 HIS Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 175 SER Chi-restraints excluded: chain b residue 227 GLU Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 263 GLN Chi-restraints excluded: chain b residue 273 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 3 optimal weight: 0.1980 chunk 72 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 8 optimal weight: 0.0970 chunk 79 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN b 50 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.179014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.126117 restraints weight = 12222.963| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.76 r_work: 0.3364 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10550 Z= 0.122 Angle : 0.586 13.729 14323 Z= 0.305 Chirality : 0.043 0.172 1546 Planarity : 0.003 0.032 1841 Dihedral : 4.368 27.050 1412 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.03 % Favored : 93.81 % Rotamer: Outliers : 3.70 % Allowed : 16.49 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -1.53 (0.23), residues: 1277 helix: 2.57 (0.42), residues: 149 sheet: -1.72 (0.34), residues: 244 loop : -1.53 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 166 TYR 0.008 0.001 TYR a 206 PHE 0.010 0.001 PHE a 217 TRP 0.006 0.001 TRP b 150 HIS 0.011 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00288 (10526) covalent geometry : angle 0.57170 (14275) SS BOND : bond 0.00196 ( 24) SS BOND : angle 2.31692 ( 48) hydrogen bonds : bond 0.03314 ( 259) hydrogen bonds : angle 4.99972 ( 699) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 118 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.8765 (tptp) cc_final: 0.8418 (tttt) REVERT: A 146 GLU cc_start: 0.8318 (pt0) cc_final: 0.7790 (mp0) REVERT: A 309 THR cc_start: 0.8214 (p) cc_final: 0.7953 (m) REVERT: B 67 MET cc_start: 0.7307 (ttp) cc_final: 0.7013 (ttp) REVERT: B 324 ARG cc_start: 0.8089 (ttp80) cc_final: 0.7466 (ttm170) REVERT: B 333 MET cc_start: 0.7334 (ttm) cc_final: 0.7104 (ttm) REVERT: B 336 ARG cc_start: 0.4356 (OUTLIER) cc_final: 0.3325 (mmp80) REVERT: a 347 ARG cc_start: 0.8673 (mtm-85) cc_final: 0.8256 (mtt-85) REVERT: b 7 ASP cc_start: 0.7117 (m-30) cc_final: 0.6562 (t0) REVERT: b 153 MET cc_start: 0.8834 (mtp) cc_final: 0.8522 (mmm) REVERT: b 263 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7149 (mt0) REVERT: b 289 GLU cc_start: 0.8086 (mp0) cc_final: 0.7694 (pm20) REVERT: b 324 ARG cc_start: 0.8126 (ttt-90) cc_final: 0.7095 (ttm170) outliers start: 42 outliers final: 34 residues processed: 151 average time/residue: 0.1048 time to fit residues: 21.7637 Evaluate side-chains 151 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 HIS Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain a residue 4 CYS Chi-restraints excluded: chain a residue 15 CYS Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain a residue 42 LEU Chi-restraints excluded: chain a residue 94 VAL Chi-restraints excluded: chain a residue 176 THR Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 243 ILE Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 273 ILE Chi-restraints excluded: chain a residue 307 LEU Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain b residue 22 HIS Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 175 SER Chi-restraints excluded: chain b residue 186 THR Chi-restraints excluded: chain b residue 227 GLU Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 263 GLN Chi-restraints excluded: chain b residue 273 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 19 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.179332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3532 r_free = 0.3532 target = 0.124613 restraints weight = 12337.040| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.26 r_work: 0.3354 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10550 Z= 0.130 Angle : 0.589 13.699 14323 Z= 0.306 Chirality : 0.043 0.155 1546 Planarity : 0.004 0.033 1841 Dihedral : 4.331 27.120 1412 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.50 % Favored : 93.34 % Rotamer: Outliers : 4.50 % Allowed : 15.70 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -1.51 (0.23), residues: 1277 helix: 2.60 (0.42), residues: 149 sheet: -1.62 (0.35), residues: 233 loop : -1.56 (0.19), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 166 TYR 0.007 0.001 TYR a 206 PHE 0.011 0.001 PHE a 217 TRP 0.006 0.001 TRP A 150 HIS 0.012 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00308 (10526) covalent geometry : angle 0.57488 (14275) SS BOND : bond 0.00193 ( 24) SS BOND : angle 2.25401 ( 48) hydrogen bonds : bond 0.03326 ( 259) hydrogen bonds : angle 4.97444 ( 699) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 116 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.8768 (tptp) cc_final: 0.8421 (tttt) REVERT: A 146 GLU cc_start: 0.8285 (pt0) cc_final: 0.7767 (mp0) REVERT: A 309 THR cc_start: 0.8213 (p) cc_final: 0.7948 (m) REVERT: B 67 MET cc_start: 0.7308 (ttp) cc_final: 0.7006 (ttp) REVERT: B 324 ARG cc_start: 0.8082 (ttp80) cc_final: 0.7441 (ttm170) REVERT: B 336 ARG cc_start: 0.4371 (OUTLIER) cc_final: 0.3488 (mtp85) REVERT: b 7 ASP cc_start: 0.7126 (m-30) cc_final: 0.6567 (t0) REVERT: b 88 VAL cc_start: 0.6453 (OUTLIER) cc_final: 0.6226 (t) REVERT: b 153 MET cc_start: 0.8828 (mtp) cc_final: 0.8512 (mmm) REVERT: b 263 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7182 (mt0) REVERT: b 289 GLU cc_start: 0.8154 (mp0) cc_final: 0.7730 (pm20) REVERT: b 324 ARG cc_start: 0.8104 (ttt-90) cc_final: 0.7075 (ttm170) outliers start: 51 outliers final: 42 residues processed: 156 average time/residue: 0.1108 time to fit residues: 23.7355 Evaluate side-chains 154 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 109 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 HIS Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain a residue 4 CYS Chi-restraints excluded: chain a residue 15 CYS Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain a residue 42 LEU Chi-restraints excluded: chain a residue 94 VAL Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 176 THR Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 243 ILE Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 273 ILE Chi-restraints excluded: chain a residue 307 LEU Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 22 HIS Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 175 SER Chi-restraints excluded: chain b residue 183 ILE Chi-restraints excluded: chain b residue 186 THR Chi-restraints excluded: chain b residue 227 GLU Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 263 GLN Chi-restraints excluded: chain b residue 273 ILE Chi-restraints excluded: chain b residue 312 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 44 optimal weight: 0.2980 chunk 64 optimal weight: 0.7980 chunk 118 optimal weight: 9.9990 chunk 50 optimal weight: 0.7980 chunk 108 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 50 HIS b 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.180012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3543 r_free = 0.3543 target = 0.126279 restraints weight = 12292.718| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.58 r_work: 0.3334 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10550 Z= 0.122 Angle : 0.595 13.316 14323 Z= 0.309 Chirality : 0.043 0.153 1546 Planarity : 0.003 0.032 1841 Dihedral : 4.317 26.905 1412 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.11 % Favored : 93.74 % Rotamer: Outliers : 4.32 % Allowed : 15.78 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -1.43 (0.23), residues: 1277 helix: 2.57 (0.42), residues: 151 sheet: -1.44 (0.34), residues: 243 loop : -1.53 (0.19), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 14 TYR 0.007 0.001 TYR a 206 PHE 0.010 0.001 PHE a 217 TRP 0.006 0.001 TRP b 150 HIS 0.011 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00287 (10526) covalent geometry : angle 0.57980 (14275) SS BOND : bond 0.00190 ( 24) SS BOND : angle 2.35519 ( 48) hydrogen bonds : bond 0.03260 ( 259) hydrogen bonds : angle 5.07454 ( 699) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 114 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.8732 (tptp) cc_final: 0.8370 (tttt) REVERT: A 146 GLU cc_start: 0.8281 (pt0) cc_final: 0.7719 (mp0) REVERT: A 309 THR cc_start: 0.8211 (p) cc_final: 0.7927 (m) REVERT: B 67 MET cc_start: 0.7276 (ttp) cc_final: 0.6957 (ttp) REVERT: B 265 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7819 (tt0) REVERT: B 298 VAL cc_start: 0.8310 (t) cc_final: 0.7966 (m) REVERT: B 324 ARG cc_start: 0.8087 (ttp80) cc_final: 0.7360 (ttm170) REVERT: B 333 MET cc_start: 0.7660 (ttm) cc_final: 0.7457 (ttm) REVERT: B 336 ARG cc_start: 0.4281 (OUTLIER) cc_final: 0.3361 (mtp85) REVERT: b 7 ASP cc_start: 0.7047 (m-30) cc_final: 0.6416 (t0) REVERT: b 133 PHE cc_start: 0.6786 (t80) cc_final: 0.6254 (t80) REVERT: b 153 MET cc_start: 0.8844 (mtp) cc_final: 0.8525 (mmm) REVERT: b 263 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7148 (mt0) REVERT: b 289 GLU cc_start: 0.8130 (mp0) cc_final: 0.7716 (pm20) REVERT: b 324 ARG cc_start: 0.8132 (ttt-90) cc_final: 0.7003 (ttm170) outliers start: 49 outliers final: 42 residues processed: 152 average time/residue: 0.1125 time to fit residues: 23.2562 Evaluate side-chains 158 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 114 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 HIS Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain a residue 4 CYS Chi-restraints excluded: chain a residue 15 CYS Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain a residue 42 LEU Chi-restraints excluded: chain a residue 94 VAL Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 176 THR Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 243 ILE Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 273 ILE Chi-restraints excluded: chain a residue 307 LEU Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 22 HIS Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 175 SER Chi-restraints excluded: chain b residue 183 ILE Chi-restraints excluded: chain b residue 186 THR Chi-restraints excluded: chain b residue 227 GLU Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 263 GLN Chi-restraints excluded: chain b residue 273 ILE Chi-restraints excluded: chain b residue 312 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 125 optimal weight: 0.0000 chunk 118 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 21 optimal weight: 0.0070 chunk 90 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 121 optimal weight: 0.0670 chunk 13 optimal weight: 3.9990 overall best weight: 0.1940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS B 76 ASN ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.183776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.137916 restraints weight = 12282.719| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.92 r_work: 0.3454 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10550 Z= 0.093 Angle : 0.568 11.828 14323 Z= 0.294 Chirality : 0.042 0.146 1546 Planarity : 0.003 0.032 1841 Dihedral : 4.171 26.292 1412 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.54 % Favored : 95.30 % Rotamer: Outliers : 2.20 % Allowed : 17.99 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -1.28 (0.23), residues: 1277 helix: 2.69 (0.42), residues: 151 sheet: -1.36 (0.34), residues: 244 loop : -1.42 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 14 TYR 0.007 0.001 TYR a 206 PHE 0.007 0.001 PHE a 217 TRP 0.005 0.001 TRP a 201 HIS 0.014 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00205 (10526) covalent geometry : angle 0.55386 (14275) SS BOND : bond 0.00179 ( 24) SS BOND : angle 2.23727 ( 48) hydrogen bonds : bond 0.02748 ( 259) hydrogen bonds : angle 5.00361 ( 699) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.8726 (tptp) cc_final: 0.8407 (tttt) REVERT: A 146 GLU cc_start: 0.8280 (pt0) cc_final: 0.7826 (mp0) REVERT: A 154 GLN cc_start: 0.9243 (tt0) cc_final: 0.9040 (tt0) REVERT: B 67 MET cc_start: 0.7321 (ttp) cc_final: 0.7023 (ttp) REVERT: B 256 ARG cc_start: 0.8257 (ptt90) cc_final: 0.7735 (ptt-90) REVERT: B 265 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7881 (tt0) REVERT: B 298 VAL cc_start: 0.8372 (t) cc_final: 0.8092 (m) REVERT: B 333 MET cc_start: 0.7607 (ttm) cc_final: 0.7253 (ttm) REVERT: B 336 ARG cc_start: 0.4293 (OUTLIER) cc_final: 0.3340 (mmp80) REVERT: a 166 ARG cc_start: 0.8332 (mtt-85) cc_final: 0.7909 (ptp-110) REVERT: b 7 ASP cc_start: 0.7150 (m-30) cc_final: 0.6598 (t0) REVERT: b 103 ARG cc_start: 0.6866 (mmp80) cc_final: 0.6580 (tpp-160) REVERT: b 133 PHE cc_start: 0.6695 (t80) cc_final: 0.6232 (t80) REVERT: b 153 MET cc_start: 0.8715 (mtp) cc_final: 0.8447 (mmm) REVERT: b 289 GLU cc_start: 0.8122 (mp0) cc_final: 0.7745 (pm20) REVERT: b 318 LEU cc_start: 0.8587 (mt) cc_final: 0.8266 (mm) outliers start: 25 outliers final: 23 residues processed: 147 average time/residue: 0.1101 time to fit residues: 22.1189 Evaluate side-chains 141 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 HIS Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain a residue 4 CYS Chi-restraints excluded: chain a residue 15 CYS Chi-restraints excluded: chain a residue 94 VAL Chi-restraints excluded: chain a residue 176 THR Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 273 ILE Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 22 HIS Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 175 SER Chi-restraints excluded: chain b residue 227 GLU Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 312 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS A 255 ASN ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.176791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.119575 restraints weight = 12285.499| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.51 r_work: 0.3301 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10550 Z= 0.197 Angle : 0.669 14.696 14323 Z= 0.348 Chirality : 0.045 0.163 1546 Planarity : 0.004 0.039 1841 Dihedral : 4.664 28.278 1412 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.05 % Favored : 92.80 % Rotamer: Outliers : 2.56 % Allowed : 18.08 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 aren not related in a simple way. whole: -1.50 (0.23), residues: 1277 helix: 2.44 (0.42), residues: 151 sheet: -1.61 (0.34), residues: 241 loop : -1.52 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 257 TYR 0.008 0.001 TYR a 32 PHE 0.013 0.002 PHE a 217 TRP 0.010 0.001 TRP A 330 HIS 0.009 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00475 (10526) covalent geometry : angle 0.65097 (14275) SS BOND : bond 0.00288 ( 24) SS BOND : angle 2.72515 ( 48) hydrogen bonds : bond 0.03790 ( 259) hydrogen bonds : angle 5.16521 ( 699) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3331.94 seconds wall clock time: 57 minutes 30.16 seconds (3450.16 seconds total)