Starting phenix.real_space_refine on Fri Feb 14 14:10:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wbh_37425/02_2025/8wbh_37425.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wbh_37425/02_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_37425/02_2025/8wbh_37425.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wbh_37425/02_2025/8wbh_37425.map" model { file = "/net/cci-nas-00/data/ceres_data/8wbh_37425/02_2025/8wbh_37425.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wbh_37425/02_2025/8wbh_37425.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.60, per 1000 atoms: 0.64 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: 2.63 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.23 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: 2.96 Time building geometry restraints manager: 3.02 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: 1.380 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: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 25.820 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.280 ------------------------------------------------------------------------------- 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 10526 Z= 0.172 Angle : 0.536 6.728 14275 Z= 0.285 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 : 6.68 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (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 TRP 0.012 0.001 TRP a 330 HIS 0.006 0.001 HIS a 340 PHE 0.009 0.001 PHE a 20 TYR 0.006 0.001 TYR a 331 ARG 0.004 0.000 ARG B 14 *********************** 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 : 1.127 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: 0.7866 (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: 0.6925 (t0) REVERT: b 207 ASN cc_start: 0.6699 (t0) cc_final: 0.6099 (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: 0.5144 (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: 0.3217 time to fit residues: 101.0142 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 : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 74 optimal weight: 0.0020 chunk 116 optimal weight: 3.9990 overall best weight: 1.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4166 r_free = 0.4166 target = 0.181221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.123132 restraints weight = 12242.051| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.80 r_work: 0.3316 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10526 Z= 0.303 Angle : 0.657 18.596 14275 Z= 0.345 Chirality : 0.046 0.187 1546 Planarity : 0.005 0.091 1841 Dihedral : 4.645 29.353 1412 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.60 % Favored : 92.25 % Rotamer: Outliers : 2.73 % Allowed : 8.02 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.23), residues: 1277 helix: 1.85 (0.43), residues: 149 sheet: -1.79 (0.34), residues: 257 loop : -1.69 (0.19), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 330 HIS 0.008 0.001 HIS B 229 PHE 0.011 0.002 PHE a 217 TYR 0.008 0.001 TYR a 331 ARG 0.005 0.001 ARG B 336 *********************** 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 176 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 1.164 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: 0.8167 (tttm) cc_final: 0.7513 (mmtp) REVERT: A 48 LYS cc_start: 0.8704 (tptp) cc_final: 0.8168 (tttt) REVERT: A 86 LEU cc_start: 0.8159 (tt) cc_final: 0.7894 (tt) REVERT: A 146 GLU cc_start: 0.8217 (pt0) cc_final: 0.7648 (mp0) REVERT: A 153 MET cc_start: 0.9291 (mtp) cc_final: 0.9081 (mmm) REVERT: A 261 LYS cc_start: 0.8657 (mttt) cc_final: 0.8385 (mtpt) REVERT: A 293 LYS cc_start: 0.8884 (mmmt) cc_final: 0.8530 (mmtt) REVERT: A 309 THR cc_start: 0.8125 (p) cc_final: 0.7908 (m) REVERT: B 33 LYS cc_start: 0.7478 (tttt) cc_final: 0.7097 (mtmt) REVERT: B 336 ARG cc_start: 0.4094 (OUTLIER) cc_final: 0.3321 (mmp80) REVERT: a 44 LYS cc_start: 0.8495 (tptt) cc_final: 0.8246 (mttt) REVERT: b 7 ASP cc_start: 0.7035 (m-30) cc_final: 0.6408 (t0) REVERT: b 263 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7136 (mt0) REVERT: b 265 GLN cc_start: 0.7448 (mt0) cc_final: 0.7080 (mm-40) REVERT: b 289 GLU cc_start: 0.8019 (mp0) cc_final: 0.7664 (pm20) REVERT: b 324 ARG cc_start: 0.8137 (ttt-90) cc_final: 0.7013 (ttm170) REVERT: b 331 TYR cc_start: 0.7325 (m-80) cc_final: 0.7020 (m-10) REVERT: b 337 PRO cc_start: 0.8445 (Cg_endo) cc_final: 0.7979 (Cg_exo) outliers start: 31 outliers final: 21 residues processed: 165 average time/residue: 0.2865 time to fit residues: 62.5878 Evaluate side-chains 152 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 300 THR Chi-restraints excluded: chain b residue 22 HIS Chi-restraints excluded: chain b residue 99 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 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 104 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN a 207 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.174605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115193 restraints weight = 12521.386| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.66 r_work: 0.3254 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.117 10526 Z= 0.602 Angle : 0.812 19.668 14275 Z= 0.429 Chirality : 0.052 0.182 1546 Planarity : 0.006 0.066 1841 Dihedral : 5.466 29.992 1412 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.87 % Favored : 89.98 % Rotamer: Outliers : 3.97 % Allowed : 14.02 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.22), residues: 1277 helix: 1.18 (0.41), residues: 149 sheet: -1.78 (0.33), residues: 264 loop : -2.05 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 330 HIS 0.013 0.002 HIS B 229 PHE 0.015 0.003 PHE A 323 TYR 0.016 0.002 TYR B 97 ARG 0.007 0.001 ARG a 172 *********************** 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 171 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 126 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8308 (tttm) cc_final: 0.7594 (mmtp) REVERT: A 48 LYS cc_start: 0.8809 (tptp) cc_final: 0.8391 (tttt) REVERT: A 86 LEU cc_start: 0.8406 (tt) cc_final: 0.8032 (tt) REVERT: A 146 GLU cc_start: 0.8335 (pt0) cc_final: 0.7793 (mp0) REVERT: A 154 GLN cc_start: 0.9219 (tt0) cc_final: 0.8911 (tt0) REVERT: A 261 LYS cc_start: 0.8697 (mttt) cc_final: 0.8468 (mtmt) REVERT: A 293 LYS cc_start: 0.9128 (mmmt) cc_final: 0.8824 (mmtm) REVERT: B 33 LYS cc_start: 0.7699 (tttt) cc_final: 0.7299 (mtmt) REVERT: B 67 MET cc_start: 0.6671 (ttp) cc_final: 0.6232 (ttt) REVERT: B 155 ILE cc_start: 0.9166 (mm) cc_final: 0.8965 (mm) REVERT: B 168 TRP cc_start: 0.7571 (m-10) cc_final: 0.7014 (m100) REVERT: B 256 ARG cc_start: 0.8470 (ptt90) cc_final: 0.7564 (ptt-90) REVERT: B 324 ARG cc_start: 0.8208 (ttp80) cc_final: 0.7389 (ttm170) REVERT: B 336 ARG cc_start: 0.4414 (OUTLIER) cc_final: 0.3727 (mmp80) REVERT: a 44 LYS cc_start: 0.8572 (tptt) cc_final: 0.8220 (ttmt) REVERT: b 265 GLN cc_start: 0.7554 (mt0) cc_final: 0.6955 (mm-40) REVERT: b 289 GLU cc_start: 0.8012 (mp0) cc_final: 0.7703 (pm20) REVERT: b 324 ARG cc_start: 0.8410 (ttt-90) cc_final: 0.7038 (ttm170) REVERT: b 331 TYR cc_start: 0.7588 (m-80) cc_final: 0.7272 (m-10) outliers start: 45 outliers final: 34 residues processed: 159 average time/residue: 0.2835 time to fit residues: 60.1269 Evaluate side-chains 142 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 107 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 197 ASP Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 310 ASP 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 22 HIS Chi-restraints excluded: chain B residue 52 GLU 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 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 288 THR Chi-restraints excluded: chain a residue 300 THR 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 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 238 GLU Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 273 ILE Chi-restraints excluded: chain b residue 334 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 0.2980 chunk 45 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 44 optimal weight: 30.0000 chunk 69 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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** B 263 GLN b 263 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.179060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.140433 restraints weight = 12353.971| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.97 r_work: 0.3349 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10526 Z= 0.227 Angle : 0.611 16.280 14275 Z= 0.320 Chirality : 0.044 0.160 1546 Planarity : 0.004 0.035 1841 Dihedral : 4.772 29.464 1412 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.26 % Favored : 93.58 % Rotamer: Outliers : 2.91 % Allowed : 16.58 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.22), residues: 1277 helix: 1.91 (0.42), residues: 149 sheet: -1.76 (0.33), residues: 263 loop : -1.86 (0.19), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 268 HIS 0.006 0.001 HIS A 22 PHE 0.011 0.002 PHE a 217 TYR 0.009 0.001 TYR a 206 ARG 0.005 0.000 ARG B 336 *********************** 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 156 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8377 (tttm) cc_final: 0.8046 (mmtt) REVERT: A 48 LYS cc_start: 0.8854 (tptp) cc_final: 0.8493 (tttt) REVERT: A 86 LEU cc_start: 0.8028 (tt) cc_final: 0.7791 (tt) REVERT: A 146 GLU cc_start: 0.8300 (pt0) cc_final: 0.7838 (mp0) REVERT: A 293 LYS cc_start: 0.8915 (mmmt) cc_final: 0.8410 (mmtm) REVERT: B 155 ILE cc_start: 0.9228 (mm) cc_final: 0.9013 (mm) REVERT: B 157 ASP cc_start: 0.7711 (p0) cc_final: 0.7477 (p0) REVERT: B 168 TRP cc_start: 0.7550 (m-10) cc_final: 0.7076 (m100) REVERT: B 256 ARG cc_start: 0.8283 (ptt90) cc_final: 0.7760 (ptt-90) REVERT: B 324 ARG cc_start: 0.8146 (ttp80) cc_final: 0.7552 (ttm170) REVERT: B 336 ARG cc_start: 0.4558 (OUTLIER) cc_final: 0.3761 (mmp80) REVERT: a 44 LYS cc_start: 0.8555 (tptt) cc_final: 0.8286 (ttmt) REVERT: b 7 ASP cc_start: 0.7324 (OUTLIER) cc_final: 0.6781 (t0) REVERT: b 265 GLN cc_start: 0.7485 (mt0) cc_final: 0.7156 (mm-40) REVERT: b 289 GLU cc_start: 0.8073 (mp0) cc_final: 0.7833 (pm20) REVERT: b 324 ARG cc_start: 0.8274 (ttt-90) cc_final: 0.7216 (ttm170) REVERT: b 331 TYR cc_start: 0.7677 (m-80) cc_final: 0.7450 (m-10) outliers start: 33 outliers final: 20 residues processed: 150 average time/residue: 0.2876 time to fit residues: 57.5368 Evaluate side-chains 136 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 1.246 ------------------------------------------------------------------------------- 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 A residue 329 CYS Chi-restraints excluded: chain B residue 22 HIS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 61 THR 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 a residue 262 THR Chi-restraints excluded: chain a residue 273 ILE Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 22 HIS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 84 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 123 optimal weight: 20.0000 chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 HIS B 147 HIS B 229 HIS a 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.175956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.119540 restraints weight = 12154.722| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.40 r_work: 0.3305 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10526 Z= 0.292 Angle : 0.628 16.082 14275 Z= 0.330 Chirality : 0.045 0.160 1546 Planarity : 0.004 0.034 1841 Dihedral : 4.778 27.850 1412 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.07 % Favored : 91.78 % Rotamer: Outliers : 3.53 % Allowed : 16.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.22), residues: 1277 helix: 2.02 (0.42), residues: 149 sheet: -1.73 (0.34), residues: 254 loop : -1.87 (0.19), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 150 HIS 0.006 0.001 HIS B 229 PHE 0.012 0.002 PHE a 217 TYR 0.009 0.001 TYR a 206 ARG 0.004 0.000 ARG B 336 *********************** 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 157 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 117 time to evaluate : 1.147 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 33 LYS cc_start: 0.8364 (tttm) cc_final: 0.7881 (mmtt) REVERT: A 48 LYS cc_start: 0.8793 (tptp) cc_final: 0.8414 (tttt) REVERT: A 86 LEU cc_start: 0.8134 (tt) cc_final: 0.7853 (tt) REVERT: A 146 GLU cc_start: 0.8284 (pt0) cc_final: 0.7855 (mp0) REVERT: A 349 GLN cc_start: 0.8587 (mm110) cc_final: 0.8161 (mm110) REVERT: B 157 ASP cc_start: 0.7691 (p0) cc_final: 0.7433 (p0) REVERT: B 168 TRP cc_start: 0.7428 (m-10) cc_final: 0.6897 (m100) REVERT: B 256 ARG cc_start: 0.8390 (ptt90) cc_final: 0.7665 (ptt-90) REVERT: B 324 ARG cc_start: 0.8133 (ttp80) cc_final: 0.7362 (ttm170) REVERT: B 336 ARG cc_start: 0.4550 (OUTLIER) cc_final: 0.3730 (mmp80) REVERT: a 44 LYS cc_start: 0.8573 (tptt) cc_final: 0.8323 (mttm) REVERT: a 106 MET cc_start: 0.8228 (tpp) cc_final: 0.7990 (tpt) REVERT: b 7 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6545 (t0) REVERT: b 265 GLN cc_start: 0.7486 (mt0) cc_final: 0.7128 (mm-40) REVERT: b 289 GLU cc_start: 0.8071 (mp0) cc_final: 0.7825 (pm20) REVERT: b 324 ARG cc_start: 0.8344 (ttt-90) cc_final: 0.7149 (ttm170) REVERT: b 331 TYR cc_start: 0.7564 (m-80) cc_final: 0.7298 (m-10) outliers start: 40 outliers final: 29 residues processed: 147 average time/residue: 0.2747 time to fit residues: 54.5057 Evaluate side-chains 143 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 1.332 ------------------------------------------------------------------------------- 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 269 ASP 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 231 LEU 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 38 THR 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 326 GLU Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 22 HIS Chi-restraints excluded: chain b residue 25 VAL 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 63 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 79 optimal weight: 0.2980 chunk 110 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN B 147 HIS B 263 GLN a 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.177168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.120277 restraints weight = 12251.129| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.50 r_work: 0.3311 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10526 Z= 0.247 Angle : 0.601 14.430 14275 Z= 0.315 Chirality : 0.044 0.156 1546 Planarity : 0.004 0.032 1841 Dihedral : 4.649 27.856 1412 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.58 % Favored : 93.27 % Rotamer: Outliers : 4.59 % Allowed : 16.58 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.22), residues: 1277 helix: 2.24 (0.43), residues: 149 sheet: -1.65 (0.34), residues: 248 loop : -1.82 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 268 HIS 0.005 0.001 HIS b 195 PHE 0.011 0.002 PHE a 217 TYR 0.008 0.001 TYR a 206 ARG 0.005 0.000 ARG a 98 *********************** 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 166 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 114 time to evaluate : 1.129 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 33 LYS cc_start: 0.8360 (tttm) cc_final: 0.7892 (mmtt) REVERT: A 48 LYS cc_start: 0.8780 (tptp) cc_final: 0.8410 (tttt) REVERT: A 86 LEU cc_start: 0.8115 (tt) cc_final: 0.7834 (tt) REVERT: A 146 GLU cc_start: 0.8261 (pt0) cc_final: 0.7828 (mp0) REVERT: A 349 GLN cc_start: 0.8617 (mm110) cc_final: 0.8248 (mm110) REVERT: B 157 ASP cc_start: 0.7563 (p0) cc_final: 0.7334 (p0) REVERT: B 168 TRP cc_start: 0.7473 (m-10) cc_final: 0.6977 (m100) REVERT: B 243 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7315 (mm) REVERT: B 256 ARG cc_start: 0.8380 (ptt90) cc_final: 0.7641 (ptt-90) REVERT: B 265 GLN cc_start: 0.8345 (mm-40) cc_final: 0.7874 (tt0) REVERT: B 324 ARG cc_start: 0.8128 (ttp80) cc_final: 0.7331 (ttm170) REVERT: B 336 ARG cc_start: 0.4618 (OUTLIER) cc_final: 0.3800 (mmp80) REVERT: a 44 LYS cc_start: 0.8568 (tptt) cc_final: 0.8316 (mttm) REVERT: b 7 ASP cc_start: 0.7194 (OUTLIER) cc_final: 0.6513 (t0) REVERT: b 153 MET cc_start: 0.8871 (mtp) cc_final: 0.8496 (mmm) REVERT: b 265 GLN cc_start: 0.7492 (mt0) cc_final: 0.7078 (mm-40) REVERT: b 289 GLU cc_start: 0.8132 (mp0) cc_final: 0.7847 (pm20) REVERT: b 324 ARG cc_start: 0.8322 (ttt-90) cc_final: 0.7127 (ttm170) REVERT: b 331 TYR cc_start: 0.7580 (m-80) cc_final: 0.7279 (m-10) outliers start: 52 outliers final: 41 residues processed: 156 average time/residue: 0.2574 time to fit residues: 54.4348 Evaluate side-chains 155 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 111 time to evaluate : 1.279 ------------------------------------------------------------------------------- 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 269 ASP 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 2 THR 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 183 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 246 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 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 301 THR Chi-restraints excluded: chain a residue 307 LEU Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 22 HIS Chi-restraints excluded: chain b residue 25 VAL 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 238 GLU 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 124 optimal weight: 6.9990 chunk 125 optimal weight: 0.0060 chunk 8 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 111 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 52 optimal weight: 0.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 HIS a 207 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.180820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 112)---------------| | r_work = 0.3553 r_free = 0.3553 target = 0.127171 restraints weight = 12398.862| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.67 r_work: 0.3342 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 10526 Z= 0.155 Angle : 0.560 12.082 14275 Z= 0.292 Chirality : 0.042 0.151 1546 Planarity : 0.003 0.031 1841 Dihedral : 4.438 26.566 1412 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.72 % Favored : 94.13 % Rotamer: Outliers : 2.65 % Allowed : 18.87 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.23), residues: 1277 helix: 2.57 (0.43), residues: 151 sheet: -1.65 (0.34), residues: 247 loop : -1.68 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 311 HIS 0.003 0.001 HIS b 195 PHE 0.009 0.001 PHE a 217 TYR 0.008 0.001 TYR a 206 ARG 0.005 0.000 ARG a 98 *********************** 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 156 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 1.153 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 33 LYS cc_start: 0.8243 (tttm) cc_final: 0.7833 (mmtm) REVERT: A 48 LYS cc_start: 0.8737 (tptp) cc_final: 0.8397 (tttt) REVERT: A 86 LEU cc_start: 0.7956 (tt) cc_final: 0.7710 (tt) REVERT: A 146 GLU cc_start: 0.8186 (pt0) cc_final: 0.7857 (mp0) REVERT: A 309 THR cc_start: 0.8180 (p) cc_final: 0.7923 (m) REVERT: B 157 ASP cc_start: 0.7283 (p0) cc_final: 0.7066 (p0) REVERT: B 168 TRP cc_start: 0.7389 (m-10) cc_final: 0.6914 (m100) REVERT: B 256 ARG cc_start: 0.8203 (ptt90) cc_final: 0.7551 (ptt-90) REVERT: B 265 GLN cc_start: 0.8138 (mm-40) cc_final: 0.7866 (tt0) REVERT: B 298 VAL cc_start: 0.8266 (t) cc_final: 0.7965 (m) REVERT: B 324 ARG cc_start: 0.7920 (ttp80) cc_final: 0.7218 (ttm170) REVERT: B 336 ARG cc_start: 0.4582 (OUTLIER) cc_final: 0.4335 (mmm160) REVERT: a 44 LYS cc_start: 0.8454 (tptt) cc_final: 0.8248 (mttt) REVERT: b 50 HIS cc_start: 0.7883 (t70) cc_final: 0.7493 (t70) REVERT: b 133 PHE cc_start: 0.6695 (t80) cc_final: 0.6064 (t80) REVERT: b 153 MET cc_start: 0.8733 (mtp) cc_final: 0.8385 (mmm) REVERT: b 265 GLN cc_start: 0.7406 (mt0) cc_final: 0.7085 (mm-40) REVERT: b 289 GLU cc_start: 0.8077 (mp0) cc_final: 0.7837 (pm20) REVERT: b 318 LEU cc_start: 0.8611 (mt) cc_final: 0.8307 (mm) REVERT: b 331 TYR cc_start: 0.7456 (m-80) cc_final: 0.7144 (m-10) outliers start: 30 outliers final: 23 residues processed: 150 average time/residue: 0.2691 time to fit residues: 54.7898 Evaluate side-chains 139 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 269 ASP Chi-restraints excluded: chain A residue 310 ASP 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 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 165 THR Chi-restraints excluded: chain a residue 176 THR Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 273 ILE Chi-restraints excluded: chain a residue 301 THR Chi-restraints excluded: chain b residue 22 HIS Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 312 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 22 optimal weight: 0.0970 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 147 HIS B 263 GLN a 207 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.179493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.126253 restraints weight = 12317.913| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.77 r_work: 0.3372 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 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 0.047 10526 Z= 0.164 Angle : 0.559 11.963 14275 Z= 0.292 Chirality : 0.042 0.147 1546 Planarity : 0.003 0.034 1841 Dihedral : 4.329 25.513 1412 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.11 % Favored : 93.74 % Rotamer: Outliers : 2.91 % Allowed : 19.22 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.23), residues: 1277 helix: 2.66 (0.42), residues: 151 sheet: -1.64 (0.33), residues: 251 loop : -1.64 (0.19), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 268 HIS 0.004 0.001 HIS B 195 PHE 0.009 0.001 PHE a 217 TYR 0.007 0.001 TYR a 206 ARG 0.007 0.000 ARG B 314 *********************** 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 146 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8433 (tttm) cc_final: 0.8072 (mmtm) REVERT: A 48 LYS cc_start: 0.8779 (tptp) cc_final: 0.8446 (tttt) REVERT: A 86 LEU cc_start: 0.7979 (tt) cc_final: 0.7731 (tt) REVERT: A 146 GLU cc_start: 0.8307 (pt0) cc_final: 0.7904 (mp0) REVERT: A 309 THR cc_start: 0.8268 (p) cc_final: 0.7960 (m) REVERT: B 256 ARG cc_start: 0.8286 (ptt90) cc_final: 0.7647 (ptt-90) REVERT: B 265 GLN cc_start: 0.8370 (mm-40) cc_final: 0.8025 (tt0) REVERT: B 298 VAL cc_start: 0.8325 (t) cc_final: 0.8058 (m) REVERT: B 324 ARG cc_start: 0.8092 (ttp80) cc_final: 0.7379 (ttm170) REVERT: B 336 ARG cc_start: 0.4661 (OUTLIER) cc_final: 0.4355 (mmm160) REVERT: a 44 LYS cc_start: 0.8545 (tptt) cc_final: 0.8319 (mttt) REVERT: a 203 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8514 (tp30) REVERT: b 7 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.6600 (t0) REVERT: b 50 HIS cc_start: 0.7890 (t70) cc_final: 0.7506 (t70) REVERT: b 133 PHE cc_start: 0.6749 (t80) cc_final: 0.6211 (t80) REVERT: b 153 MET cc_start: 0.8810 (mtp) cc_final: 0.8506 (mmm) REVERT: b 265 GLN cc_start: 0.7492 (mt0) cc_final: 0.7219 (mm-40) REVERT: b 289 GLU cc_start: 0.8112 (mp0) cc_final: 0.7844 (pm20) REVERT: b 331 TYR cc_start: 0.7502 (m-80) cc_final: 0.7170 (m-10) outliers start: 33 outliers final: 26 residues processed: 141 average time/residue: 0.2653 time to fit residues: 51.0711 Evaluate side-chains 139 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 321 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain B residue 54 VAL 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 57 VAL 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 203 GLU Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 273 ILE Chi-restraints excluded: chain a residue 301 THR Chi-restraints excluded: chain a residue 307 LEU Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 22 HIS Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 238 GLU 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 119 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS A 91 ASN B 147 HIS a 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.173500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.119982 restraints weight = 12491.411| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.70 r_work: 0.3273 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.097 10526 Z= 0.571 Angle : 0.794 16.744 14275 Z= 0.418 Chirality : 0.051 0.179 1546 Planarity : 0.005 0.052 1841 Dihedral : 5.301 26.080 1412 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.87 % Favored : 89.98 % Rotamer: Outliers : 4.32 % Allowed : 17.99 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.22), residues: 1277 helix: 1.84 (0.42), residues: 149 sheet: -1.84 (0.32), residues: 270 loop : -1.92 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 150 HIS 0.015 0.002 HIS A 22 PHE 0.017 0.003 PHE a 217 TYR 0.013 0.002 TYR a 32 ARG 0.007 0.001 ARG A 314 *********************** 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 156 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 107 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8368 (tttm) cc_final: 0.7938 (mmtp) REVERT: A 48 LYS cc_start: 0.8867 (tptp) cc_final: 0.8494 (tttt) REVERT: A 86 LEU cc_start: 0.8149 (tt) cc_final: 0.7827 (tt) REVERT: B 67 MET cc_start: 0.6717 (ttp) cc_final: 0.6311 (ttt) REVERT: B 231 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.7494 (pt) REVERT: B 243 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7217 (mm) REVERT: B 256 ARG cc_start: 0.8438 (ptt90) cc_final: 0.7748 (ptt-90) REVERT: B 298 VAL cc_start: 0.8309 (t) cc_final: 0.8030 (m) REVERT: B 324 ARG cc_start: 0.8354 (ttp80) cc_final: 0.7534 (ttm170) REVERT: B 336 ARG cc_start: 0.5188 (OUTLIER) cc_final: 0.4829 (mmm160) REVERT: a 44 LYS cc_start: 0.8588 (tptt) cc_final: 0.8334 (mttm) REVERT: a 146 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7728 (tm-30) REVERT: b 7 ASP cc_start: 0.7207 (OUTLIER) cc_final: 0.6502 (t0) REVERT: b 265 GLN cc_start: 0.7678 (mt0) cc_final: 0.7165 (mm-40) REVERT: b 289 GLU cc_start: 0.8246 (mp0) cc_final: 0.7840 (pm20) REVERT: b 324 ARG cc_start: 0.8422 (ttt-90) cc_final: 0.7255 (ttm170) REVERT: b 331 TYR cc_start: 0.7802 (m-80) cc_final: 0.7582 (m-10) outliers start: 49 outliers final: 40 residues processed: 149 average time/residue: 0.2652 time to fit residues: 54.5814 Evaluate side-chains 145 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 101 time to evaluate : 1.238 ------------------------------------------------------------------------------- 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 307 LEU Chi-restraints excluded: chain A residue 310 ASP 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 54 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 246 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 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 301 THR Chi-restraints excluded: chain a residue 307 LEU Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 22 HIS Chi-restraints excluded: chain b residue 25 VAL 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 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 90 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS B 154 GLN B 263 GLN a 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.179042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3552 r_free = 0.3552 target = 0.127252 restraints weight = 12376.600| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.63 r_work: 0.3327 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10526 Z= 0.194 Angle : 0.606 13.273 14275 Z= 0.318 Chirality : 0.043 0.172 1546 Planarity : 0.004 0.031 1841 Dihedral : 4.638 27.021 1412 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.19 % Favored : 93.66 % Rotamer: Outliers : 2.82 % Allowed : 20.02 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.23), residues: 1277 helix: 2.37 (0.42), residues: 151 sheet: -1.56 (0.34), residues: 245 loop : -1.73 (0.19), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 330 HIS 0.005 0.001 HIS b 195 PHE 0.010 0.001 PHE a 217 TYR 0.007 0.001 TYR a 206 ARG 0.006 0.000 ARG a 98 ********************** 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 143 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8385 (tttm) cc_final: 0.7958 (mmtt) REVERT: A 48 LYS cc_start: 0.8785 (tptp) cc_final: 0.8440 (tttt) REVERT: A 86 LEU cc_start: 0.8048 (tt) cc_final: 0.7782 (tt) REVERT: A 146 GLU cc_start: 0.8295 (pt0) cc_final: 0.7893 (mp0) REVERT: A 293 LYS cc_start: 0.8951 (mmmt) cc_final: 0.8569 (mttp) REVERT: A 309 THR cc_start: 0.8197 (p) cc_final: 0.7872 (m) REVERT: B 168 TRP cc_start: 0.7529 (m-10) cc_final: 0.7246 (m-10) REVERT: B 256 ARG cc_start: 0.8415 (ptt90) cc_final: 0.7672 (ptt-90) REVERT: B 298 VAL cc_start: 0.8294 (t) cc_final: 0.7993 (m) REVERT: B 324 ARG cc_start: 0.8186 (ttp80) cc_final: 0.7403 (ttm170) REVERT: B 336 ARG cc_start: 0.5213 (OUTLIER) cc_final: 0.4769 (mmm160) REVERT: a 44 LYS cc_start: 0.8569 (tptt) cc_final: 0.8305 (mttm) REVERT: a 333 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8231 (ttp) REVERT: b 7 ASP cc_start: 0.7101 (OUTLIER) cc_final: 0.6396 (t0) REVERT: b 50 HIS cc_start: 0.7898 (t70) cc_final: 0.7528 (t70) REVERT: b 103 ARG cc_start: 0.7369 (mmt90) cc_final: 0.7010 (mmt90) REVERT: b 153 MET cc_start: 0.8881 (mtp) cc_final: 0.8521 (mmm) REVERT: b 265 GLN cc_start: 0.7532 (mt0) cc_final: 0.7118 (mm-40) REVERT: b 289 GLU cc_start: 0.8246 (mp0) cc_final: 0.7838 (pm20) REVERT: b 324 ARG cc_start: 0.8291 (ttt-90) cc_final: 0.7117 (ttm170) REVERT: b 331 TYR cc_start: 0.7614 (m-80) cc_final: 0.7369 (m-10) outliers start: 32 outliers final: 27 residues processed: 136 average time/residue: 0.2743 time to fit residues: 50.6268 Evaluate side-chains 140 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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 310 ASP 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 54 VAL Chi-restraints excluded: chain B residue 61 THR 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 38 THR 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 262 THR Chi-restraints excluded: chain a residue 301 THR Chi-restraints excluded: chain a residue 307 LEU Chi-restraints excluded: chain a residue 333 MET Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 22 HIS Chi-restraints excluded: chain b residue 71 VAL 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 66 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 39 optimal weight: 0.0870 chunk 28 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 207 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.178572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3554 r_free = 0.3554 target = 0.125294 restraints weight = 12234.325| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.81 r_work: 0.3344 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10526 Z= 0.201 Angle : 0.597 13.049 14275 Z= 0.312 Chirality : 0.043 0.151 1546 Planarity : 0.004 0.033 1841 Dihedral : 4.558 25.883 1412 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.97 % Favored : 92.87 % Rotamer: Outliers : 3.26 % Allowed : 19.66 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.23), residues: 1277 helix: 2.51 (0.42), residues: 151 sheet: -1.61 (0.34), residues: 245 loop : -1.70 (0.19), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 330 HIS 0.006 0.001 HIS A 22 PHE 0.011 0.001 PHE a 217 TYR 0.008 0.001 TYR a 206 ARG 0.006 0.000 ARG a 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6582.07 seconds wall clock time: 117 minutes 1.10 seconds (7021.10 seconds total)