Starting phenix.real_space_refine on Sat Jul 20 07:28:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbh_37425/07_2024/8wbh_37425.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbh_37425/07_2024/8wbh_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbh_37425/07_2024/8wbh_37425.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbh_37425/07_2024/8wbh_37425.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbh_37425/07_2024/8wbh_37425.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbh_37425/07_2024/8wbh_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 Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 5.93, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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: 3.68 Conformation dependent library (CDL) restraints added in 1.8 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: 1.28 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: 2.72 Time building geometry restraints manager: 4.09 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: 100.52 - 107.23: 442 107.23 - 113.93: 5941 113.93 - 120.63: 3721 120.63 - 127.33: 3988 127.33 - 134.03: 183 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 2.440 nonbonded pdb=" O GLY a 266 " pdb=" OG SER a 348 " model vdw 2.251 2.440 nonbonded pdb=" OG1 THR b 286 " pdb=" O TRP b 311 " model vdw 2.289 2.440 nonbonded pdb=" OE2 GLU B 26 " pdb=" NH2 ARG B 214 " model vdw 2.301 2.520 nonbonded pdb=" OG1 THR A 302 " pdb=" O THR A 344 " model vdw 2.302 2.440 ... (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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 107 or resid 133 throu \ gh 207 or (resid 208 and (name N or name CA or name C or name O or name CB )) or \ resid 209 through 338)) selection = chain 'B' selection = (chain 'a' and (resid 1 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 107 or resid 133 throu \ gh 207 or (resid 208 and (name N or name CA or name C or name O or name CB )) or \ resid 209 through 338)) selection = (chain 'b' and (resid 1 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 107 or resid 133 throu \ gh 207 or (resid 208 and (name N or name CA or name C or name O or name CB )) or \ resid 209 through 338)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.930 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.490 Find NCS groups from input model: 0.560 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10526 Z= 0.172 Angle : 0.536 6.728 14275 Z= 0.285 Chirality : 0.043 0.184 1546 Planarity : 0.003 0.043 1841 Dihedral : 11.714 86.694 3887 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.03 % Favored : 93.81 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.22), residues: 1277 helix: 1.90 (0.44), residues: 145 sheet: -1.50 (0.37), residues: 223 loop : -1.71 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 330 HIS 0.006 0.001 HIS a 340 PHE 0.009 0.001 PHE a 20 TYR 0.006 0.001 TYR a 331 ARG 0.004 0.000 ARG B 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 1.231 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: 0.3071 time to fit residues: 96.4770 Evaluate side-chains 143 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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: 10.0000 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 74 optimal weight: 0.0370 chunk 116 optimal weight: 2.9990 overall best weight: 1.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 263 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10526 Z= 0.278 Angle : 0.634 19.300 14275 Z= 0.332 Chirality : 0.045 0.164 1546 Planarity : 0.005 0.061 1841 Dihedral : 4.552 29.731 1412 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.28 % Favored : 92.56 % Rotamer: Outliers : 2.73 % Allowed : 8.29 % Favored : 88.98 % 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: -1.83 (0.22), residues: 1277 helix: 1.91 (0.43), residues: 149 sheet: -1.78 (0.34), residues: 250 loop : -1.70 (0.19), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 330 HIS 0.008 0.001 HIS A 22 PHE 0.010 0.002 PHE a 217 TYR 0.007 0.001 TYR a 206 ARG 0.005 0.001 ARG a 14 *********************** 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 177 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 146 time to evaluate : 1.094 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: 0.8222 (tttm) cc_final: 0.7673 (mmtp) REVERT: A 48 LYS cc_start: 0.8724 (tptp) cc_final: 0.8168 (tttt) REVERT: A 86 LEU cc_start: 0.8113 (tt) cc_final: 0.7856 (tt) REVERT: A 146 GLU cc_start: 0.7954 (pt0) cc_final: 0.7638 (mp0) REVERT: A 261 LYS cc_start: 0.8516 (mttt) cc_final: 0.8316 (mtpt) REVERT: A 293 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8503 (mmtt) REVERT: B 33 LYS cc_start: 0.7407 (tttt) cc_final: 0.7163 (mtmt) REVERT: B 136 ASP cc_start: 0.6899 (t0) cc_final: 0.6555 (p0) REVERT: B 298 VAL cc_start: 0.8332 (p) cc_final: 0.8021 (m) REVERT: B 336 ARG cc_start: 0.3789 (OUTLIER) cc_final: 0.3145 (mmp80) REVERT: b 7 ASP cc_start: 0.6904 (m-30) cc_final: 0.6460 (t0) REVERT: b 263 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7166 (mt0) REVERT: b 265 GLN cc_start: 0.7436 (mt0) cc_final: 0.7060 (mm-40) REVERT: b 289 GLU cc_start: 0.8059 (mp0) cc_final: 0.7752 (pm20) REVERT: b 324 ARG cc_start: 0.8025 (ttt-90) cc_final: 0.7025 (ttm170) REVERT: b 337 PRO cc_start: 0.8461 (Cg_endo) cc_final: 0.8008 (Cg_exo) outliers start: 31 outliers final: 21 residues processed: 166 average time/residue: 0.2736 time to fit residues: 60.5144 Evaluate side-chains 152 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 1.124 ------------------------------------------------------------------------------- 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 a residue 4 CYS Chi-restraints excluded: chain a residue 15 CYS Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 94 VAL Chi-restraints excluded: chain a residue 176 THR Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 243 ILE Chi-restraints excluded: chain a residue 288 THR 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 64 optimal weight: 3.9990 chunk 36 optimal weight: 0.0770 chunk 96 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 0.0060 chunk 116 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 HIS B 154 GLN ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN b 263 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10526 Z= 0.173 Angle : 0.558 15.809 14275 Z= 0.291 Chirality : 0.042 0.151 1546 Planarity : 0.004 0.047 1841 Dihedral : 4.266 29.681 1412 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.79 % Favored : 94.05 % Rotamer: Outliers : 2.47 % Allowed : 12.43 % Favored : 85.10 % 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: 2.25 (0.43), residues: 149 sheet: -1.53 (0.33), residues: 254 loop : -1.66 (0.19), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP b 330 HIS 0.004 0.001 HIS B 195 PHE 0.009 0.001 PHE a 217 TYR 0.009 0.001 TYR b 331 ARG 0.006 0.000 ARG B 314 *********************** 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 166 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 138 time to evaluate : 1.268 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: 0.8250 (tttm) cc_final: 0.7829 (mttm) REVERT: A 48 LYS cc_start: 0.8693 (tptp) cc_final: 0.8322 (tttt) REVERT: A 86 LEU cc_start: 0.8110 (tt) cc_final: 0.7870 (tt) REVERT: A 146 GLU cc_start: 0.7944 (pt0) cc_final: 0.7634 (mp0) REVERT: A 261 LYS cc_start: 0.8523 (mttt) cc_final: 0.8319 (mtpt) REVERT: A 293 LYS cc_start: 0.8707 (mmmt) cc_final: 0.8459 (mmmt) REVERT: B 136 ASP cc_start: 0.6931 (t0) cc_final: 0.6607 (p0) REVERT: B 256 ARG cc_start: 0.8245 (ptt90) cc_final: 0.7647 (ptt-90) REVERT: B 298 VAL cc_start: 0.8337 (p) cc_final: 0.8005 (m) REVERT: B 336 ARG cc_start: 0.3885 (OUTLIER) cc_final: 0.3275 (mtp85) REVERT: b 7 ASP cc_start: 0.6997 (m-30) cc_final: 0.6367 (t0) REVERT: b 265 GLN cc_start: 0.7407 (mt0) cc_final: 0.7052 (mm-40) REVERT: b 289 GLU cc_start: 0.8059 (mp0) cc_final: 0.7752 (pm20) REVERT: b 324 ARG cc_start: 0.7939 (ttt-90) cc_final: 0.6941 (ttm170) REVERT: b 331 TYR cc_start: 0.7367 (m-10) cc_final: 0.7079 (m-10) outliers start: 28 outliers final: 21 residues processed: 155 average time/residue: 0.2867 time to fit residues: 59.0442 Evaluate side-chains 145 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 1.294 ------------------------------------------------------------------------------- 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 B residue 22 HIS Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain a residue 4 CYS Chi-restraints excluded: chain a residue 15 CYS Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 94 VAL Chi-restraints excluded: chain a residue 176 THR Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 243 ILE Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain b residue 22 HIS Chi-restraints excluded: chain b residue 143 CYS Chi-restraints excluded: chain b residue 227 GLU Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 262 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 12 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 123 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS B 22 HIS ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 263 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10526 Z= 0.172 Angle : 0.543 14.194 14275 Z= 0.283 Chirality : 0.042 0.149 1546 Planarity : 0.003 0.035 1841 Dihedral : 4.206 28.144 1412 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.19 % Favored : 93.66 % Rotamer: Outliers : 3.17 % Allowed : 14.02 % Favored : 82.80 % 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: -1.58 (0.22), residues: 1277 helix: 2.46 (0.43), residues: 149 sheet: -1.58 (0.34), residues: 239 loop : -1.62 (0.19), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 330 HIS 0.004 0.001 HIS B 22 PHE 0.009 0.001 PHE a 217 TYR 0.007 0.001 TYR a 206 ARG 0.007 0.000 ARG b 14 *********************** 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 168 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 132 time to evaluate : 1.080 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: 0.8247 (tttm) cc_final: 0.7852 (mttm) REVERT: A 48 LYS cc_start: 0.8684 (tptp) cc_final: 0.8321 (tttt) REVERT: A 86 LEU cc_start: 0.8114 (tt) cc_final: 0.7856 (tt) REVERT: A 146 GLU cc_start: 0.7993 (pt0) cc_final: 0.7689 (mp0) REVERT: B 136 ASP cc_start: 0.6927 (t0) cc_final: 0.6613 (p0) REVERT: B 256 ARG cc_start: 0.8226 (ptt90) cc_final: 0.7625 (ptt-90) REVERT: B 298 VAL cc_start: 0.8298 (p) cc_final: 0.7988 (m) REVERT: B 336 ARG cc_start: 0.3809 (OUTLIER) cc_final: 0.3222 (mtp85) REVERT: b 7 ASP cc_start: 0.6978 (m-30) cc_final: 0.6357 (t0) REVERT: b 265 GLN cc_start: 0.7466 (mt0) cc_final: 0.7081 (mm-40) REVERT: b 289 GLU cc_start: 0.8072 (mp0) cc_final: 0.7728 (pm20) REVERT: b 324 ARG cc_start: 0.7930 (ttt-90) cc_final: 0.6951 (ttm170) outliers start: 36 outliers final: 26 residues processed: 157 average time/residue: 0.2676 time to fit residues: 56.7217 Evaluate side-chains 150 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 123 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 HIS Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain B residue 22 HIS Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 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 55 CYS Chi-restraints excluded: chain a residue 94 VAL Chi-restraints excluded: chain a residue 176 THR Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 243 ILE Chi-restraints excluded: chain a residue 300 THR Chi-restraints excluded: chain b residue 22 HIS Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 175 SER Chi-restraints excluded: chain b residue 227 GLU Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 262 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 111 optimal weight: 0.0670 chunk 31 optimal weight: 3.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 HIS B 147 HIS ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10526 Z= 0.323 Angle : 0.624 15.182 14275 Z= 0.326 Chirality : 0.045 0.163 1546 Planarity : 0.004 0.036 1841 Dihedral : 4.583 27.250 1412 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.91 % Favored : 91.93 % Rotamer: Outliers : 3.44 % Allowed : 16.05 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.22), residues: 1277 helix: 2.33 (0.42), residues: 149 sheet: -1.63 (0.34), residues: 243 loop : -1.72 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 330 HIS 0.015 0.002 HIS A 22 PHE 0.013 0.002 PHE A 323 TYR 0.009 0.001 TYR a 206 ARG 0.006 0.000 ARG a 166 *********************** 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 159 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 120 time to evaluate : 1.154 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: A 33 LYS cc_start: 0.8276 (tttm) cc_final: 0.7858 (mttm) REVERT: A 48 LYS cc_start: 0.8716 (tptp) cc_final: 0.8370 (tttt) REVERT: A 86 LEU cc_start: 0.8167 (tt) cc_final: 0.7887 (tt) REVERT: A 146 GLU cc_start: 0.8026 (pt0) cc_final: 0.7699 (mp0) REVERT: B 136 ASP cc_start: 0.6971 (t0) cc_final: 0.6561 (p0) REVERT: B 298 VAL cc_start: 0.8328 (p) cc_final: 0.8040 (m) REVERT: B 336 ARG cc_start: 0.3842 (OUTLIER) cc_final: 0.3240 (mtp85) REVERT: b 7 ASP cc_start: 0.6956 (m-30) cc_final: 0.6297 (t0) REVERT: b 265 GLN cc_start: 0.7552 (mt0) cc_final: 0.7103 (mm-40) REVERT: b 289 GLU cc_start: 0.8076 (mp0) cc_final: 0.7749 (pm20) REVERT: b 324 ARG cc_start: 0.8110 (ttt-90) cc_final: 0.7046 (ttm170) outliers start: 39 outliers final: 31 residues processed: 150 average time/residue: 0.2657 time to fit residues: 53.3704 Evaluate side-chains 149 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 117 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 HIS Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 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 54 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain a residue 4 CYS Chi-restraints excluded: chain a residue 15 CYS Chi-restraints excluded: chain a residue 42 LEU Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 94 VAL Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 176 THR Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 243 ILE Chi-restraints excluded: chain a residue 288 THR Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain b residue 22 HIS Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 143 CYS Chi-restraints excluded: chain b residue 175 SER Chi-restraints excluded: chain b residue 227 GLU Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 262 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 123 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 10 optimal weight: 0.0670 chunk 40 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS B 22 HIS ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10526 Z= 0.177 Angle : 0.551 13.655 14275 Z= 0.288 Chirality : 0.042 0.151 1546 Planarity : 0.003 0.032 1841 Dihedral : 4.281 27.178 1412 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.11 % Favored : 93.74 % Rotamer: Outliers : 3.88 % Allowed : 16.05 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.23), residues: 1277 helix: 2.63 (0.43), residues: 149 sheet: -1.71 (0.34), residues: 245 loop : -1.58 (0.19), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 330 HIS 0.004 0.001 HIS B 229 PHE 0.010 0.001 PHE a 217 TYR 0.008 0.001 TYR a 206 ARG 0.005 0.000 ARG a 166 *********************** 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 163 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 119 time to evaluate : 1.255 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: 0.8261 (tttm) cc_final: 0.7821 (mmtt) REVERT: A 48 LYS cc_start: 0.8701 (tptp) cc_final: 0.8371 (tttt) REVERT: A 86 LEU cc_start: 0.8140 (tt) cc_final: 0.7863 (tt) REVERT: A 146 GLU cc_start: 0.8021 (pt0) cc_final: 0.7723 (mp0) REVERT: A 293 LYS cc_start: 0.8895 (mmmt) cc_final: 0.8334 (mmmt) REVERT: B 136 ASP cc_start: 0.6947 (t0) cc_final: 0.6595 (p0) REVERT: B 298 VAL cc_start: 0.8321 (OUTLIER) cc_final: 0.8078 (m) REVERT: B 336 ARG cc_start: 0.3928 (OUTLIER) cc_final: 0.3258 (mtp85) REVERT: b 7 ASP cc_start: 0.6952 (m-30) cc_final: 0.6376 (t0) REVERT: b 88 VAL cc_start: 0.6634 (OUTLIER) cc_final: 0.6425 (t) REVERT: b 153 MET cc_start: 0.8772 (mtp) cc_final: 0.8395 (mmm) REVERT: b 265 GLN cc_start: 0.7510 (mt0) cc_final: 0.7074 (mm-40) REVERT: b 289 GLU cc_start: 0.8050 (mp0) cc_final: 0.7721 (pm20) REVERT: b 324 ARG cc_start: 0.8037 (ttt-90) cc_final: 0.6971 (ttm170) outliers start: 44 outliers final: 33 residues processed: 154 average time/residue: 0.2547 time to fit residues: 53.5134 Evaluate side-chains 150 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 114 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 HIS Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 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 196 SER Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 231 LEU 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 42 LEU Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 94 VAL Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 176 THR Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 243 ILE Chi-restraints excluded: chain a residue 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 b residue 22 HIS Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain b residue 143 CYS Chi-restraints excluded: chain b residue 175 SER Chi-restraints excluded: chain b residue 227 GLU Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 262 THR 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 119 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 HIS b 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 10526 Z= 0.456 Angle : 0.698 16.175 14275 Z= 0.366 Chirality : 0.048 0.176 1546 Planarity : 0.005 0.045 1841 Dihedral : 4.896 26.512 1412 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.55 % Favored : 90.29 % Rotamer: Outliers : 4.32 % Allowed : 16.84 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.22), residues: 1277 helix: 2.08 (0.42), residues: 149 sheet: -1.94 (0.32), residues: 269 loop : -1.77 (0.19), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 330 HIS 0.020 0.002 HIS A 22 PHE 0.015 0.002 PHE A 323 TYR 0.010 0.002 TYR a 32 ARG 0.005 0.001 ARG A 314 *********************** 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 167 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 118 time to evaluate : 1.141 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: 0.8271 (tttm) cc_final: 0.7874 (mttm) REVERT: A 48 LYS cc_start: 0.8754 (tptp) cc_final: 0.8399 (tttt) REVERT: A 86 LEU cc_start: 0.8194 (tt) cc_final: 0.7880 (tt) REVERT: A 340 HIS cc_start: 0.6962 (t-90) cc_final: 0.6509 (t-90) REVERT: B 136 ASP cc_start: 0.6938 (t0) cc_final: 0.6452 (p0) REVERT: B 231 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7185 (pt) REVERT: B 298 VAL cc_start: 0.8357 (OUTLIER) cc_final: 0.8112 (m) REVERT: B 324 ARG cc_start: 0.8082 (ttp80) cc_final: 0.7295 (ttm170) REVERT: B 336 ARG cc_start: 0.4309 (OUTLIER) cc_final: 0.3670 (mmp80) REVERT: b 7 ASP cc_start: 0.6950 (m-30) cc_final: 0.6285 (t0) REVERT: b 88 VAL cc_start: 0.6673 (OUTLIER) cc_final: 0.6468 (t) REVERT: b 153 MET cc_start: 0.8840 (mtp) cc_final: 0.8415 (mmm) REVERT: b 265 GLN cc_start: 0.7573 (mt0) cc_final: 0.7173 (mm-40) REVERT: b 289 GLU cc_start: 0.8107 (mp0) cc_final: 0.7729 (pm20) REVERT: b 324 ARG cc_start: 0.8214 (ttt-90) cc_final: 0.7025 (ttm170) outliers start: 49 outliers final: 38 residues processed: 156 average time/residue: 0.2753 time to fit residues: 57.7680 Evaluate side-chains 152 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 110 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 HIS Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 314 ARG 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 55 CYS Chi-restraints excluded: chain a residue 94 VAL Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 176 THR Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 243 ILE Chi-restraints excluded: chain a residue 300 THR Chi-restraints excluded: chain a residue 307 LEU Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain b residue 22 HIS Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 143 CYS Chi-restraints excluded: chain b residue 175 SER Chi-restraints excluded: chain b residue 183 ILE Chi-restraints excluded: chain b residue 186 THR Chi-restraints excluded: chain b residue 227 GLU Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 273 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.0870 chunk 73 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS a 207 ASN ** b 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10526 Z= 0.169 Angle : 0.559 13.714 14275 Z= 0.291 Chirality : 0.043 0.152 1546 Planarity : 0.003 0.032 1841 Dihedral : 4.358 27.485 1412 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.72 % Favored : 94.13 % Rotamer: Outliers : 3.44 % Allowed : 18.08 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.23), residues: 1277 helix: 2.46 (0.42), residues: 151 sheet: -1.75 (0.34), residues: 251 loop : -1.56 (0.19), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 330 HIS 0.005 0.001 HIS b 195 PHE 0.008 0.001 PHE a 217 TYR 0.008 0.001 TYR a 206 ARG 0.004 0.000 ARG a 166 *********************** 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 153 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 114 time to evaluate : 1.178 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: A 33 LYS cc_start: 0.8233 (tttm) cc_final: 0.7818 (mmtt) REVERT: A 48 LYS cc_start: 0.8701 (tptp) cc_final: 0.8370 (tttt) REVERT: A 86 LEU cc_start: 0.8154 (tt) cc_final: 0.7891 (tt) REVERT: A 340 HIS cc_start: 0.6865 (t-90) cc_final: 0.6358 (t-90) REVERT: B 136 ASP cc_start: 0.6892 (t0) cc_final: 0.6545 (p0) REVERT: B 298 VAL cc_start: 0.8338 (OUTLIER) cc_final: 0.8119 (m) REVERT: B 336 ARG cc_start: 0.4236 (OUTLIER) cc_final: 0.3604 (mmp80) REVERT: a 7 ASP cc_start: 0.8007 (t0) cc_final: 0.7510 (m-30) REVERT: b 7 ASP cc_start: 0.6785 (m-30) cc_final: 0.6194 (t0) REVERT: b 153 MET cc_start: 0.8784 (mtp) cc_final: 0.8435 (mmm) REVERT: b 265 GLN cc_start: 0.7519 (mt0) cc_final: 0.7010 (mm-40) REVERT: b 289 GLU cc_start: 0.8071 (mp0) cc_final: 0.7705 (pm20) REVERT: b 324 ARG cc_start: 0.8109 (ttt-90) cc_final: 0.7005 (ttm170) outliers start: 39 outliers final: 34 residues processed: 145 average time/residue: 0.2574 time to fit residues: 50.7311 Evaluate side-chains 146 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 110 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 HIS Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 314 ARG 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 55 CYS Chi-restraints excluded: chain a residue 94 VAL Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 176 THR Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 243 ILE Chi-restraints excluded: chain a residue 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 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 143 CYS Chi-restraints excluded: chain b residue 175 SER Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 273 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 69 optimal weight: 0.0370 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 HIS a 207 ASN ** b 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 10526 Z= 0.404 Angle : 0.674 15.722 14275 Z= 0.352 Chirality : 0.047 0.168 1546 Planarity : 0.005 0.040 1841 Dihedral : 4.788 26.747 1412 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.40 % Favored : 90.45 % Rotamer: Outliers : 3.88 % Allowed : 18.34 % Favored : 77.78 % 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: -1.85 (0.23), residues: 1277 helix: 2.10 (0.42), residues: 151 sheet: -1.90 (0.33), residues: 260 loop : -1.71 (0.19), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 330 HIS 0.019 0.002 HIS A 22 PHE 0.015 0.002 PHE A 323 TYR 0.009 0.001 TYR a 206 ARG 0.004 0.001 ARG b 205 *********************** 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 147 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 103 time to evaluate : 1.315 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: 0.8262 (tttm) cc_final: 0.7832 (mmtt) REVERT: A 48 LYS cc_start: 0.8709 (tptp) cc_final: 0.8360 (tttt) REVERT: A 86 LEU cc_start: 0.8191 (tt) cc_final: 0.7874 (tt) REVERT: B 136 ASP cc_start: 0.6910 (t0) cc_final: 0.6480 (p0) REVERT: B 168 TRP cc_start: 0.7407 (m-10) cc_final: 0.7001 (m100) REVERT: B 231 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7131 (pt) REVERT: B 336 ARG cc_start: 0.4400 (OUTLIER) cc_final: 0.4200 (mmm160) REVERT: b 7 ASP cc_start: 0.6875 (m-30) cc_final: 0.6228 (t0) REVERT: b 153 MET cc_start: 0.8830 (mtp) cc_final: 0.8439 (mmm) REVERT: b 265 GLN cc_start: 0.7543 (mt0) cc_final: 0.7153 (mm-40) REVERT: b 289 GLU cc_start: 0.8145 (mp0) cc_final: 0.7748 (pm20) REVERT: b 324 ARG cc_start: 0.8216 (ttt-90) cc_final: 0.7030 (ttm170) outliers start: 44 outliers final: 36 residues processed: 139 average time/residue: 0.2823 time to fit residues: 53.0623 Evaluate side-chains 138 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 100 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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 99 SER 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 321 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 314 ARG 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 55 CYS Chi-restraints excluded: chain a residue 94 VAL Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 243 ILE Chi-restraints excluded: chain a residue 288 THR Chi-restraints excluded: chain a residue 307 LEU Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain b residue 22 HIS Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 143 CYS Chi-restraints excluded: chain b residue 175 SER Chi-restraints excluded: chain b residue 183 ILE Chi-restraints excluded: chain b residue 186 THR Chi-restraints excluded: chain b residue 227 GLU Chi-restraints excluded: chain b residue 273 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 10 optimal weight: 0.0170 chunk 78 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 108 optimal weight: 10.0000 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS B 76 ASN B 147 HIS a 207 ASN ** b 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10526 Z= 0.162 Angle : 0.555 12.600 14275 Z= 0.289 Chirality : 0.042 0.146 1546 Planarity : 0.003 0.032 1841 Dihedral : 4.299 27.373 1412 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.56 % Favored : 94.28 % Rotamer: Outliers : 3.44 % Allowed : 18.52 % Favored : 78.04 % 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: -1.56 (0.23), residues: 1277 helix: 2.49 (0.43), residues: 151 sheet: -1.63 (0.35), residues: 239 loop : -1.60 (0.19), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 330 HIS 0.004 0.001 HIS b 195 PHE 0.009 0.001 PHE a 217 TYR 0.008 0.001 TYR a 206 ARG 0.004 0.000 ARG a 172 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 113 time to evaluate : 1.315 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: 0.8247 (tttm) cc_final: 0.7829 (mmtm) REVERT: A 48 LYS cc_start: 0.8694 (tptp) cc_final: 0.8330 (tttt) REVERT: A 86 LEU cc_start: 0.8142 (tt) cc_final: 0.7884 (tt) REVERT: A 293 LYS cc_start: 0.8874 (mmmt) cc_final: 0.8238 (mmmm) REVERT: B 168 TRP cc_start: 0.7333 (m-10) cc_final: 0.6887 (m100) REVERT: B 336 ARG cc_start: 0.4372 (OUTLIER) cc_final: 0.4136 (mmm160) REVERT: a 7 ASP cc_start: 0.8037 (t0) cc_final: 0.7547 (m-30) REVERT: b 7 ASP cc_start: 0.6774 (m-30) cc_final: 0.6193 (t0) REVERT: b 153 MET cc_start: 0.8780 (mtp) cc_final: 0.8446 (mmm) REVERT: b 265 GLN cc_start: 0.7440 (mt0) cc_final: 0.7017 (mm-40) REVERT: b 289 GLU cc_start: 0.8087 (mp0) cc_final: 0.7717 (pm20) REVERT: b 324 ARG cc_start: 0.8146 (ttt-90) cc_final: 0.7019 (ttm170) outliers start: 39 outliers final: 33 residues processed: 144 average time/residue: 0.2573 time to fit residues: 50.2773 Evaluate side-chains 141 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 107 time to evaluate : 1.220 ------------------------------------------------------------------------------- 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 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 228 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 314 ARG 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 288 THR Chi-restraints excluded: chain a residue 307 LEU Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain b residue 22 HIS Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 143 CYS Chi-restraints excluded: chain b residue 175 SER Chi-restraints excluded: chain b residue 273 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 0.0770 chunk 93 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 HIS a 207 ASN ** b 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.178865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.3505 r_free = 0.3505 target = 0.123920 restraints weight = 12340.010| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.79 r_work: 0.3303 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10526 Z= 0.240 Angle : 0.589 13.756 14275 Z= 0.306 Chirality : 0.044 0.156 1546 Planarity : 0.004 0.038 1841 Dihedral : 4.392 26.877 1412 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.05 % Favored : 92.80 % Rotamer: Outliers : 3.44 % Allowed : 18.78 % Favored : 77.78 % 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: -1.56 (0.23), residues: 1277 helix: 2.43 (0.42), residues: 151 sheet: -1.72 (0.35), residues: 238 loop : -1.55 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 330 HIS 0.012 0.001 HIS A 22 PHE 0.011 0.002 PHE a 217 TYR 0.008 0.001 TYR a 206 ARG 0.005 0.000 ARG a 172 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2605.56 seconds wall clock time: 47 minutes 2.56 seconds (2822.56 seconds total)