Starting phenix.real_space_refine on Mon Jun 9 04:58:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wbh_37425/06_2025/8wbh_37425.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wbh_37425/06_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_37425/06_2025/8wbh_37425.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wbh_37425/06_2025/8wbh_37425.map" model { file = "/net/cci-nas-00/data/ceres_data/8wbh_37425/06_2025/8wbh_37425.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wbh_37425/06_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-5710/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: 6.80, per 1000 atoms: 0.66 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: 2.44 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: 1.15 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: 2.69 Time building geometry restraints manager: 2.98 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: 23.100 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: 26.010 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10550 Z= 0.116 Angle : 0.542 6.728 14323 Z= 0.288 Chirality : 0.043 0.184 1546 Planarity : 0.003 0.043 1841 Dihedral : 11.714 86.694 3887 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.68 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 Details of bonding type rmsd hydrogen bonds : bond 0.21277 ( 259) hydrogen bonds : angle 7.93699 ( 699) SS BOND : bond 0.00268 ( 24) SS BOND : angle 1.47853 ( 48) covalent geometry : bond 0.00254 (10526) covalent geometry : angle 0.53609 (14275) *********************** 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 : 1.228 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: 0.3088 time to fit residues: 97.1267 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 : 1.224 ------------------------------------------------------------------------------- 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: 7.9990 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: 2.9990 chunk 74 optimal weight: 0.0020 chunk 116 optimal weight: 3.9990 overall best weight: 2.1594 ------------------------------------------------------------------------------- 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 = 0.4155 r_free = 0.4155 target = 0.180130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.120958 restraints weight = 12247.045| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.87 r_work: 0.3304 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10550 Z= 0.220 Angle : 0.712 19.978 14323 Z= 0.372 Chirality : 0.047 0.194 1546 Planarity : 0.005 0.096 1841 Dihedral : 4.753 29.454 1412 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.83 % Favored : 92.01 % Rotamer: Outliers : 2.65 % Allowed : 8.55 % Favored : 88.80 % 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: -1.93 (0.22), residues: 1277 helix: 1.75 (0.42), residues: 149 sheet: -1.91 (0.33), residues: 269 loop : -1.71 (0.19), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 330 HIS 0.009 0.002 HIS B 229 PHE 0.011 0.002 PHE A 323 TYR 0.010 0.001 TYR a 32 ARG 0.006 0.001 ARG B 336 Details of bonding type rmsd hydrogen bonds : bond 0.04755 ( 259) hydrogen bonds : angle 5.77095 ( 699) SS BOND : bond 0.00331 ( 24) SS BOND : angle 3.24170 ( 48) covalent geometry : bond 0.00531 (10526) covalent geometry : angle 0.68768 (14275) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 1.145 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: 0.8163 (tttm) cc_final: 0.7494 (mmtp) REVERT: A 48 LYS cc_start: 0.8735 (tptp) cc_final: 0.8170 (tttt) REVERT: A 86 LEU cc_start: 0.8169 (tt) cc_final: 0.7899 (tt) REVERT: A 146 GLU cc_start: 0.8202 (pt0) cc_final: 0.7745 (mp0) REVERT: A 153 MET cc_start: 0.9320 (mtp) cc_final: 0.9089 (mmm) REVERT: A 261 LYS cc_start: 0.8655 (mttt) cc_final: 0.8375 (mtpt) REVERT: A 293 LYS cc_start: 0.8863 (mmmt) cc_final: 0.8610 (mmmt) REVERT: A 309 THR cc_start: 0.8149 (p) cc_final: 0.7905 (m) REVERT: B 33 LYS cc_start: 0.7491 (tttt) cc_final: 0.7112 (mtmt) REVERT: B 168 TRP cc_start: 0.7336 (m-10) cc_final: 0.6789 (m100) REVERT: B 298 VAL cc_start: 0.8333 (p) cc_final: 0.8023 (m) REVERT: B 324 ARG cc_start: 0.7749 (ttp80) cc_final: 0.7184 (ttm170) REVERT: B 336 ARG cc_start: 0.4149 (OUTLIER) cc_final: 0.3303 (mmp80) REVERT: a 44 LYS cc_start: 0.8499 (tptt) cc_final: 0.8258 (mttt) REVERT: b 7 ASP cc_start: 0.7064 (m-30) cc_final: 0.6398 (t0) REVERT: b 102 LYS cc_start: 0.8338 (mttt) cc_final: 0.8101 (mttp) REVERT: b 263 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.7123 (mt0) REVERT: b 265 GLN cc_start: 0.7507 (mt0) cc_final: 0.7128 (mm-40) REVERT: b 289 GLU cc_start: 0.8006 (mp0) cc_final: 0.7669 (pm20) REVERT: b 324 ARG cc_start: 0.8171 (ttt-90) cc_final: 0.7016 (ttm170) REVERT: b 331 TYR cc_start: 0.7383 (m-80) cc_final: 0.7075 (m-10) REVERT: b 337 PRO cc_start: 0.8449 (Cg_endo) cc_final: 0.7973 (Cg_exo) outliers start: 30 outliers final: 20 residues processed: 165 average time/residue: 0.2851 time to fit residues: 62.1847 Evaluate side-chains 153 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 1.218 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 72 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 154 GLN ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN a 207 ASN b 263 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.177266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.117806 restraints weight = 12444.425| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.66 r_work: 0.3281 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 10550 Z= 0.269 Angle : 0.729 18.392 14323 Z= 0.382 Chirality : 0.048 0.170 1546 Planarity : 0.005 0.044 1841 Dihedral : 5.030 30.089 1412 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.30 % Favored : 91.54 % Rotamer: Outliers : 3.44 % Allowed : 13.58 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.10 (0.22), residues: 1277 helix: 1.55 (0.42), residues: 149 sheet: -1.86 (0.33), residues: 273 loop : -1.88 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 150 HIS 0.011 0.002 HIS B 229 PHE 0.013 0.002 PHE A 323 TYR 0.011 0.002 TYR a 32 ARG 0.005 0.001 ARG a 172 Details of bonding type rmsd hydrogen bonds : bond 0.04766 ( 259) hydrogen bonds : angle 5.56537 ( 699) SS BOND : bond 0.00431 ( 24) SS BOND : angle 2.73513 ( 48) covalent geometry : bond 0.00651 (10526) covalent geometry : angle 0.71274 (14275) *********************** 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 172 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 1.138 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: 0.8279 (tttm) cc_final: 0.7603 (mmtp) REVERT: A 48 LYS cc_start: 0.8772 (tptp) cc_final: 0.8364 (tttt) REVERT: A 86 LEU cc_start: 0.8341 (tt) cc_final: 0.7993 (tt) REVERT: A 146 GLU cc_start: 0.8347 (pt0) cc_final: 0.7802 (mp0) REVERT: A 153 MET cc_start: 0.9360 (mtp) cc_final: 0.9082 (mmm) REVERT: A 261 LYS cc_start: 0.8717 (mttt) cc_final: 0.8467 (mtmt) REVERT: A 314 ARG cc_start: 0.6992 (ttm-80) cc_final: 0.6710 (ttt-90) REVERT: B 33 LYS cc_start: 0.7542 (tttt) cc_final: 0.7218 (mtmt) REVERT: B 155 ILE cc_start: 0.9158 (mm) cc_final: 0.8949 (mm) REVERT: B 168 TRP cc_start: 0.7513 (m-10) cc_final: 0.6974 (m100) REVERT: B 298 VAL cc_start: 0.8238 (p) cc_final: 0.7873 (m) REVERT: B 324 ARG cc_start: 0.8146 (ttp80) cc_final: 0.7344 (ttm170) REVERT: B 336 ARG cc_start: 0.4300 (OUTLIER) cc_final: 0.3521 (mtp85) REVERT: a 44 LYS cc_start: 0.8567 (tptt) cc_final: 0.8219 (ttmt) REVERT: b 265 GLN cc_start: 0.7602 (mt0) cc_final: 0.7104 (mm-40) REVERT: b 289 GLU cc_start: 0.7968 (mp0) cc_final: 0.7594 (pm20) REVERT: b 324 ARG cc_start: 0.8325 (ttt-90) cc_final: 0.6994 (ttm170) REVERT: b 331 TYR cc_start: 0.7479 (m-80) cc_final: 0.7163 (m-10) outliers start: 39 outliers final: 27 residues processed: 160 average time/residue: 0.2718 time to fit residues: 58.6031 Evaluate side-chains 145 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 1.092 ------------------------------------------------------------------------------- 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 288 THR 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 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 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 300 THR Chi-restraints excluded: chain a residue 307 LEU 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 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: 0.9990 chunk 45 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 121 optimal weight: 0.0270 chunk 114 optimal weight: 0.6980 chunk 38 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 44 optimal weight: 30.0000 chunk 69 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 overall best weight: 0.4840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN B 22 HIS B 147 HIS ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.180131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.123388 restraints weight = 12188.112| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.49 r_work: 0.3349 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10550 Z= 0.099 Angle : 0.580 14.993 14323 Z= 0.303 Chirality : 0.042 0.153 1546 Planarity : 0.003 0.035 1841 Dihedral : 4.384 29.324 1412 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.64 % Favored : 94.21 % Rotamer: Outliers : 2.47 % Allowed : 15.52 % 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: -1.76 (0.23), residues: 1277 helix: 2.23 (0.43), residues: 149 sheet: -1.72 (0.33), residues: 266 loop : -1.70 (0.19), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 268 HIS 0.004 0.001 HIS B 22 PHE 0.009 0.001 PHE a 217 TYR 0.008 0.001 TYR a 206 ARG 0.005 0.000 ARG b 72 Details of bonding type rmsd hydrogen bonds : bond 0.03393 ( 259) hydrogen bonds : angle 5.15721 ( 699) SS BOND : bond 0.00220 ( 24) SS BOND : angle 2.30042 ( 48) covalent geometry : bond 0.00220 (10526) covalent geometry : angle 0.56566 (14275) *********************** 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 163 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 1.356 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: 0.8239 (tttm) cc_final: 0.7835 (mmtt) REVERT: A 48 LYS cc_start: 0.8752 (tptp) cc_final: 0.8411 (tttt) REVERT: A 86 LEU cc_start: 0.8002 (tt) cc_final: 0.7770 (tt) REVERT: A 146 GLU cc_start: 0.8254 (pt0) cc_final: 0.7787 (mp0) REVERT: A 309 THR cc_start: 0.8171 (p) cc_final: 0.7954 (m) REVERT: B 155 ILE cc_start: 0.9150 (mm) cc_final: 0.8931 (mm) REVERT: B 157 ASP cc_start: 0.7611 (p0) cc_final: 0.7300 (p0) REVERT: B 168 TRP cc_start: 0.7373 (m-10) cc_final: 0.6880 (m100) REVERT: B 256 ARG cc_start: 0.8133 (ptt90) cc_final: 0.7583 (ptt-90) REVERT: B 298 VAL cc_start: 0.8351 (p) cc_final: 0.8067 (m) REVERT: B 324 ARG cc_start: 0.7971 (ttp80) cc_final: 0.7350 (ttm170) REVERT: B 336 ARG cc_start: 0.4227 (OUTLIER) cc_final: 0.3316 (mtp85) REVERT: b 153 MET cc_start: 0.8745 (mtp) cc_final: 0.8383 (mmm) REVERT: b 265 GLN cc_start: 0.7473 (mt0) cc_final: 0.7166 (mm-40) REVERT: b 289 GLU cc_start: 0.8058 (mp0) cc_final: 0.7681 (pm20) REVERT: b 324 ARG cc_start: 0.8163 (ttt-90) cc_final: 0.7128 (ttm170) REVERT: b 331 TYR cc_start: 0.7459 (m-80) cc_final: 0.7250 (m-10) outliers start: 28 outliers final: 17 residues processed: 159 average time/residue: 0.3756 time to fit residues: 80.5034 Evaluate side-chains 136 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 1.510 ------------------------------------------------------------------------------- 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 336 ARG Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain a residue 4 CYS Chi-restraints excluded: chain a residue 15 CYS Chi-restraints excluded: chain a residue 94 VAL Chi-restraints excluded: chain a residue 176 THR Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 273 ILE Chi-restraints excluded: chain a residue 288 THR Chi-restraints excluded: chain a residue 329 CYS Chi-restraints excluded: chain b residue 22 HIS Chi-restraints excluded: chain b residue 186 THR 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: 1.9990 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 123 optimal weight: 20.0000 chunk 85 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS B 147 HIS B 229 HIS B 263 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.176919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 125)---------------| | r_work = 0.3517 r_free = 0.3517 target = 0.123936 restraints weight = 12247.846| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.30 r_work: 0.3293 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 10550 Z= 0.210 Angle : 0.666 16.113 14323 Z= 0.349 Chirality : 0.046 0.205 1546 Planarity : 0.004 0.046 1841 Dihedral : 4.769 27.641 1412 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.30 % Favored : 91.54 % Rotamer: Outliers : 3.53 % Allowed : 16.75 % Favored : 79.72 % 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: -1.86 (0.22), residues: 1277 helix: 2.14 (0.43), residues: 149 sheet: -1.73 (0.34), residues: 255 loop : -1.79 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 330 HIS 0.007 0.001 HIS B 229 PHE 0.013 0.002 PHE a 323 TYR 0.009 0.001 TYR a 206 ARG 0.008 0.001 ARG a 166 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 259) hydrogen bonds : angle 5.27891 ( 699) SS BOND : bond 0.00299 ( 24) SS BOND : angle 2.55657 ( 48) covalent geometry : bond 0.00510 (10526) covalent geometry : angle 0.65050 (14275) *********************** 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 153 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 113 time to evaluate : 1.227 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: 0.8385 (tttm) cc_final: 0.8078 (mmtt) REVERT: A 48 LYS cc_start: 0.8799 (tptp) cc_final: 0.8467 (tttt) REVERT: A 86 LEU cc_start: 0.8075 (tt) cc_final: 0.7802 (tt) REVERT: A 146 GLU cc_start: 0.8360 (pt0) cc_final: 0.7958 (mp0) REVERT: A 309 THR cc_start: 0.8328 (p) cc_final: 0.8042 (m) REVERT: B 157 ASP cc_start: 0.7758 (p0) cc_final: 0.7465 (p0) REVERT: B 168 TRP cc_start: 0.7542 (m-10) cc_final: 0.7075 (m100) REVERT: B 231 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7282 (pt) REVERT: B 298 VAL cc_start: 0.8385 (p) cc_final: 0.8147 (m) REVERT: B 324 ARG cc_start: 0.8193 (ttp80) cc_final: 0.7551 (ttm170) REVERT: B 336 ARG cc_start: 0.4612 (OUTLIER) cc_final: 0.3717 (mmp80) REVERT: b 7 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.6746 (t0) REVERT: b 265 GLN cc_start: 0.7677 (mt0) cc_final: 0.7264 (mm-40) REVERT: b 289 GLU cc_start: 0.8131 (mp0) cc_final: 0.7669 (pm20) REVERT: b 324 ARG cc_start: 0.8277 (ttt-90) cc_final: 0.7209 (ttm170) REVERT: b 331 TYR cc_start: 0.7668 (m-80) cc_final: 0.7442 (m-10) outliers start: 40 outliers final: 32 residues processed: 145 average time/residue: 0.2619 time to fit residues: 51.4618 Evaluate side-chains 147 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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 313 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain a residue 4 CYS Chi-restraints excluded: chain a residue 15 CYS Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain a residue 42 LEU Chi-restraints excluded: chain a residue 94 VAL Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 176 THR Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 243 ILE Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain a residue 329 CYS 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 71 VAL Chi-restraints excluded: chain b residue 175 SER Chi-restraints excluded: chain b residue 186 THR Chi-restraints excluded: chain b residue 227 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 63 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 105 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 46 optimal weight: 9.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS B 147 HIS B 263 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.177486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.138761 restraints weight = 12369.668| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.03 r_work: 0.3334 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10550 Z= 0.160 Angle : 0.628 15.269 14323 Z= 0.329 Chirality : 0.045 0.164 1546 Planarity : 0.004 0.039 1841 Dihedral : 4.645 27.882 1412 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.81 % Favored : 93.03 % Rotamer: Outliers : 4.14 % Allowed : 17.55 % Favored : 78.31 % 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: -1.73 (0.23), residues: 1277 helix: 2.26 (0.42), residues: 149 sheet: -1.68 (0.32), residues: 278 loop : -1.68 (0.19), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 150 HIS 0.010 0.001 HIS A 22 PHE 0.012 0.002 PHE a 217 TYR 0.008 0.001 TYR a 206 ARG 0.006 0.000 ARG a 166 Details of bonding type rmsd hydrogen bonds : bond 0.03732 ( 259) hydrogen bonds : angle 5.16275 ( 699) SS BOND : bond 0.00229 ( 24) SS BOND : angle 2.43516 ( 48) covalent geometry : bond 0.00385 (10526) covalent geometry : angle 0.61252 (14275) *********************** 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 159 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 112 time to evaluate : 1.176 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: 0.8399 (tttm) cc_final: 0.8099 (mmtt) REVERT: A 48 LYS cc_start: 0.8823 (tptp) cc_final: 0.8495 (tttt) REVERT: A 86 LEU cc_start: 0.7981 (tt) cc_final: 0.7748 (tt) REVERT: A 146 GLU cc_start: 0.8325 (pt0) cc_final: 0.7939 (mp0) REVERT: A 309 THR cc_start: 0.8270 (p) cc_final: 0.8029 (m) REVERT: B 298 VAL cc_start: 0.8422 (OUTLIER) cc_final: 0.8222 (m) REVERT: B 324 ARG cc_start: 0.8148 (ttp80) cc_final: 0.7546 (ttm170) REVERT: B 336 ARG cc_start: 0.4640 (OUTLIER) cc_final: 0.3747 (mmp80) REVERT: a 14 ARG cc_start: 0.7030 (mtp85) cc_final: 0.6689 (ttp80) REVERT: b 265 GLN cc_start: 0.7532 (mt0) cc_final: 0.7244 (mm-40) REVERT: b 289 GLU cc_start: 0.8128 (mp0) cc_final: 0.7654 (pm20) REVERT: b 324 ARG cc_start: 0.8208 (ttt-90) cc_final: 0.7213 (ttm170) REVERT: b 331 TYR cc_start: 0.7682 (m-80) cc_final: 0.7463 (m-10) outliers start: 47 outliers final: 35 residues processed: 149 average time/residue: 0.2813 time to fit residues: 56.2853 Evaluate side-chains 146 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 313 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 298 VAL 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 288 THR Chi-restraints excluded: chain a residue 307 LEU Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain a residue 329 CYS Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 22 HIS Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 186 THR Chi-restraints excluded: chain b residue 227 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: 5.9990 chunk 125 optimal weight: 0.0970 chunk 8 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 59 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS B 147 HIS B 263 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.178739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.124365 restraints weight = 12365.718| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.80 r_work: 0.3345 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10550 Z= 0.110 Angle : 0.587 13.599 14323 Z= 0.306 Chirality : 0.043 0.151 1546 Planarity : 0.003 0.033 1841 Dihedral : 4.390 27.212 1412 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.34 % Favored : 93.50 % Rotamer: Outliers : 3.62 % Allowed : 17.99 % Favored : 78.40 % 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: -1.61 (0.23), residues: 1277 helix: 2.52 (0.42), residues: 149 sheet: -1.66 (0.33), residues: 258 loop : -1.62 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 268 HIS 0.010 0.001 HIS A 22 PHE 0.010 0.001 PHE a 217 TYR 0.008 0.001 TYR a 206 ARG 0.006 0.000 ARG a 166 Details of bonding type rmsd hydrogen bonds : bond 0.03238 ( 259) hydrogen bonds : angle 4.98370 ( 699) SS BOND : bond 0.00207 ( 24) SS BOND : angle 2.24489 ( 48) covalent geometry : bond 0.00256 (10526) covalent geometry : angle 0.57292 (14275) *********************** 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: 41 poor density : 115 time to evaluate : 1.216 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: 0.8399 (tttm) cc_final: 0.7985 (mmtm) REVERT: A 48 LYS cc_start: 0.8749 (tptp) cc_final: 0.8390 (tttt) REVERT: A 86 LEU cc_start: 0.8050 (tt) cc_final: 0.7795 (tt) REVERT: A 146 GLU cc_start: 0.8301 (pt0) cc_final: 0.7746 (mp0) REVERT: A 309 THR cc_start: 0.8274 (p) cc_final: 0.7999 (m) REVERT: B 157 ASP cc_start: 0.7438 (p0) cc_final: 0.7151 (p0) REVERT: B 168 TRP cc_start: 0.7529 (m-10) cc_final: 0.7017 (m100) REVERT: B 324 ARG cc_start: 0.8109 (ttp80) cc_final: 0.7391 (ttm170) REVERT: B 336 ARG cc_start: 0.4511 (OUTLIER) cc_final: 0.3418 (mmp80) REVERT: b 7 ASP cc_start: 0.7167 (OUTLIER) cc_final: 0.6507 (t0) REVERT: b 50 HIS cc_start: 0.7940 (t70) cc_final: 0.7524 (t70) REVERT: b 133 PHE cc_start: 0.6833 (t80) cc_final: 0.6099 (t80) REVERT: b 153 MET cc_start: 0.8855 (mtp) cc_final: 0.8501 (mmm) REVERT: b 265 GLN cc_start: 0.7514 (mt0) cc_final: 0.7193 (mm-40) REVERT: b 289 GLU cc_start: 0.8068 (mp0) cc_final: 0.7670 (pm20) REVERT: b 324 ARG cc_start: 0.8181 (ttt-90) cc_final: 0.7078 (ttm170) REVERT: b 331 TYR cc_start: 0.7570 (m-80) cc_final: 0.7258 (m-10) outliers start: 41 outliers final: 34 residues processed: 148 average time/residue: 0.2616 time to fit residues: 52.8387 Evaluate side-chains 149 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 HIS Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain a residue 4 CYS Chi-restraints excluded: chain a residue 15 CYS Chi-restraints excluded: chain a residue 42 LEU Chi-restraints excluded: chain a residue 94 VAL Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 176 THR Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 243 ILE Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 273 ILE Chi-restraints excluded: chain a residue 307 LEU Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain a residue 329 CYS 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 99 SER Chi-restraints excluded: chain b residue 183 ILE Chi-restraints excluded: chain b residue 186 THR 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: 4.9990 chunk 31 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS B 147 HIS B 263 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.177275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.138386 restraints weight = 12470.158| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.98 r_work: 0.3341 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10550 Z= 0.170 Angle : 0.634 14.558 14323 Z= 0.330 Chirality : 0.045 0.155 1546 Planarity : 0.004 0.034 1841 Dihedral : 4.574 26.983 1412 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.36 % Favored : 92.48 % Rotamer: Outliers : 4.14 % Allowed : 17.46 % Favored : 78.40 % 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: 2.45 (0.42), residues: 149 sheet: -1.54 (0.33), residues: 259 loop : -1.70 (0.19), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 150 HIS 0.013 0.001 HIS A 22 PHE 0.012 0.002 PHE a 217 TYR 0.008 0.001 TYR a 206 ARG 0.006 0.000 ARG a 166 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 259) hydrogen bonds : angle 5.10829 ( 699) SS BOND : bond 0.00273 ( 24) SS BOND : angle 2.49891 ( 48) covalent geometry : bond 0.00411 (10526) covalent geometry : angle 0.61816 (14275) *********************** 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 160 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 113 time to evaluate : 1.167 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: 0.8377 (tttm) cc_final: 0.8102 (mmtt) REVERT: A 48 LYS cc_start: 0.8802 (tptp) cc_final: 0.8503 (tttt) REVERT: A 86 LEU cc_start: 0.7936 (tt) cc_final: 0.7701 (tt) REVERT: A 146 GLU cc_start: 0.8299 (pt0) cc_final: 0.7937 (mp0) REVERT: A 309 THR cc_start: 0.8271 (p) cc_final: 0.8059 (m) REVERT: B 231 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7191 (pt) REVERT: B 324 ARG cc_start: 0.8198 (ttp80) cc_final: 0.7532 (ttm170) REVERT: B 336 ARG cc_start: 0.4747 (OUTLIER) cc_final: 0.3565 (mmp80) REVERT: b 7 ASP cc_start: 0.7320 (OUTLIER) cc_final: 0.6709 (t0) REVERT: b 265 GLN cc_start: 0.7495 (mt0) cc_final: 0.7218 (mm-40) REVERT: b 289 GLU cc_start: 0.8202 (mp0) cc_final: 0.7747 (pm20) REVERT: b 331 TYR cc_start: 0.7661 (m-80) cc_final: 0.7402 (m-10) outliers start: 47 outliers final: 37 residues processed: 151 average time/residue: 0.2814 time to fit residues: 57.0333 Evaluate side-chains 148 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 1.152 ------------------------------------------------------------------------------- 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 313 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 17 SER 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 196 SER Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain a residue 4 CYS Chi-restraints excluded: chain a residue 15 CYS Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain a residue 42 LEU Chi-restraints excluded: chain a residue 94 VAL Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 176 THR Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 243 ILE Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 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 183 ILE Chi-restraints excluded: chain b residue 186 THR Chi-restraints excluded: chain b residue 227 GLU Chi-restraints excluded: chain b residue 273 ILE Chi-restraints excluded: chain b residue 312 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 113 optimal weight: 0.4980 chunk 41 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS B 147 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.177213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.122774 restraints weight = 12258.457| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.75 r_work: 0.3309 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10550 Z= 0.147 Angle : 0.618 14.283 14323 Z= 0.323 Chirality : 0.044 0.154 1546 Planarity : 0.004 0.041 1841 Dihedral : 4.524 26.936 1412 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.89 % Favored : 92.95 % Rotamer: Outliers : 3.97 % Allowed : 17.64 % Favored : 78.40 % 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: 149 sheet: -1.65 (0.35), residues: 236 loop : -1.68 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 150 HIS 0.008 0.001 HIS A 22 PHE 0.011 0.002 PHE a 217 TYR 0.008 0.001 TYR a 206 ARG 0.006 0.000 ARG a 98 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 259) hydrogen bonds : angle 5.09940 ( 699) SS BOND : bond 0.00218 ( 24) SS BOND : angle 2.45056 ( 48) covalent geometry : bond 0.00353 (10526) covalent geometry : angle 0.60294 (14275) *********************** 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 151 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 106 time to evaluate : 1.145 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: 0.8422 (tttm) cc_final: 0.7995 (mmtm) REVERT: A 48 LYS cc_start: 0.8775 (tptp) cc_final: 0.8442 (tttt) REVERT: A 86 LEU cc_start: 0.8062 (tt) cc_final: 0.7801 (tt) REVERT: A 146 GLU cc_start: 0.8285 (pt0) cc_final: 0.7862 (mp0) REVERT: A 309 THR cc_start: 0.8289 (p) cc_final: 0.8009 (m) REVERT: B 243 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7317 (mm) REVERT: B 324 ARG cc_start: 0.8174 (ttp80) cc_final: 0.7402 (ttm170) REVERT: B 336 ARG cc_start: 0.4805 (OUTLIER) cc_final: 0.4337 (mmm160) REVERT: a 203 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8551 (tp30) REVERT: b 7 ASP cc_start: 0.7227 (OUTLIER) cc_final: 0.6551 (t0) REVERT: b 50 HIS cc_start: 0.7897 (t70) cc_final: 0.7492 (t70) REVERT: b 133 PHE cc_start: 0.6996 (t80) cc_final: 0.6280 (t80) REVERT: b 153 MET cc_start: 0.8871 (mtp) cc_final: 0.8516 (mmm) REVERT: b 265 GLN cc_start: 0.7501 (mt0) cc_final: 0.7170 (mm-40) REVERT: b 289 GLU cc_start: 0.8153 (mp0) cc_final: 0.7721 (pm20) REVERT: b 331 TYR cc_start: 0.7628 (m-80) cc_final: 0.7412 (m-10) outliers start: 45 outliers final: 40 residues processed: 144 average time/residue: 0.2858 time to fit residues: 57.1455 Evaluate side-chains 149 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 105 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 313 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 17 SER 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 196 SER Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 243 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 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 203 GLU 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 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 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 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: 1.9990 chunk 100 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 1 optimal weight: 0.4980 chunk 80 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 7 optimal weight: 0.0570 overall best weight: 1.7104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.176240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.119438 restraints weight = 12324.031| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.76 r_work: 0.3276 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10550 Z= 0.175 Angle : 0.640 14.728 14323 Z= 0.334 Chirality : 0.045 0.156 1546 Planarity : 0.004 0.033 1841 Dihedral : 4.606 26.873 1412 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.36 % Favored : 92.48 % Rotamer: Outliers : 4.23 % Allowed : 17.55 % Favored : 78.22 % 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: -1.68 (0.23), residues: 1277 helix: 2.44 (0.42), residues: 151 sheet: -1.65 (0.35), residues: 236 loop : -1.71 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 150 HIS 0.009 0.001 HIS A 22 PHE 0.012 0.002 PHE a 217 TYR 0.008 0.001 TYR a 206 ARG 0.006 0.000 ARG a 98 Details of bonding type rmsd hydrogen bonds : bond 0.03629 ( 259) hydrogen bonds : angle 5.13270 ( 699) SS BOND : bond 0.00247 ( 24) SS BOND : angle 2.51152 ( 48) covalent geometry : bond 0.00424 (10526) covalent geometry : angle 0.62380 (14275) ********************** 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 156 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 108 time to evaluate : 1.167 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: 0.8240 (tttm) cc_final: 0.7829 (mmtt) REVERT: A 48 LYS cc_start: 0.8733 (tptp) cc_final: 0.8403 (tttt) REVERT: A 86 LEU cc_start: 0.8002 (tt) cc_final: 0.7753 (tt) REVERT: A 146 GLU cc_start: 0.8186 (pt0) cc_final: 0.7850 (mp0) REVERT: A 309 THR cc_start: 0.8206 (p) cc_final: 0.7950 (m) REVERT: B 231 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.6996 (pt) REVERT: B 243 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.7195 (mm) REVERT: B 324 ARG cc_start: 0.8056 (ttp80) cc_final: 0.7285 (ttm170) REVERT: B 336 ARG cc_start: 0.4932 (OUTLIER) cc_final: 0.4461 (mmm160) REVERT: a 203 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8411 (tp30) REVERT: b 7 ASP cc_start: 0.7186 (OUTLIER) cc_final: 0.6513 (t0) REVERT: b 153 MET cc_start: 0.8797 (mtp) cc_final: 0.8405 (mmm) REVERT: b 265 GLN cc_start: 0.7485 (mt0) cc_final: 0.7116 (mm-40) REVERT: b 289 GLU cc_start: 0.8162 (mp0) cc_final: 0.7740 (pm20) REVERT: b 324 ARG cc_start: 0.8235 (ttt-90) cc_final: 0.7096 (ttm170) outliers start: 48 outliers final: 41 residues processed: 149 average time/residue: 0.2881 time to fit residues: 59.2520 Evaluate side-chains 152 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 106 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 HIS Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 17 SER 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 196 SER Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 243 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 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 203 GLU 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 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 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 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: 3.9990 chunk 86 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS B 147 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.175682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 115)---------------| | r_work = 0.3496 r_free = 0.3496 target = 0.120738 restraints weight = 12315.768| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.89 r_work: 0.3300 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 10550 Z= 0.232 Angle : 0.690 15.815 14323 Z= 0.361 Chirality : 0.047 0.170 1546 Planarity : 0.004 0.037 1841 Dihedral : 4.846 26.852 1412 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.30 % Favored : 91.54 % Rotamer: Outliers : 4.14 % Allowed : 17.72 % Favored : 78.13 % 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: -1.86 (0.22), residues: 1277 helix: 2.25 (0.42), residues: 151 sheet: -1.86 (0.33), residues: 248 loop : -1.78 (0.19), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 150 HIS 0.016 0.002 HIS A 22 PHE 0.013 0.002 PHE a 217 TYR 0.013 0.001 TYR b 331 ARG 0.006 0.001 ARG a 98 Details of bonding type rmsd hydrogen bonds : bond 0.04055 ( 259) hydrogen bonds : angle 5.25984 ( 699) SS BOND : bond 0.00306 ( 24) SS BOND : angle 2.68241 ( 48) covalent geometry : bond 0.00564 (10526) covalent geometry : angle 0.67388 (14275) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7027.81 seconds wall clock time: 122 minutes 59.89 seconds (7379.89 seconds total)