Starting phenix.real_space_refine on Thu Mar 13 11:57:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ljd_23391/03_2025/7ljd_23391.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ljd_23391/03_2025/7ljd_23391.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/7ljd_23391/03_2025/7ljd_23391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ljd_23391/03_2025/7ljd_23391.map" model { file = "/net/cci-nas-00/data/ceres_data/7ljd_23391/03_2025/7ljd_23391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ljd_23391/03_2025/7ljd_23391.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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 56 5.16 5 Cl 2 4.86 5 C 5468 2.51 5 N 1447 2.21 5 O 1545 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8518 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2269 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 3 Chain: "A" Number of atoms: 1987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1987 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 253 Unusual residues: {'CLR': 5, 'G4C': 1, 'LDP': 1, 'PLM': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1 LDP R 501 " occ=0.50 ... (9 atoms not shown) pdb=" O2 LDP R 501 " occ=0.50 Time building chain proxies: 5.50, per 1000 atoms: 0.65 Number of scatterers: 8518 At special positions: 0 Unit cell: (95.316, 99.372, 121.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 56 16.00 O 1545 8.00 N 1447 7.00 C 5468 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS R 298 " - pdb=" SG CYS R 307 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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: 2.42 Conformation dependent library (CDL) restraints added in 1.1 seconds 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1984 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 10 sheets defined 43.4% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'R' and resid 21 through 50 removed outlier: 4.292A pdb=" N LEU R 25 " --> pdb=" O SER R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 57 removed outlier: 4.131A pdb=" N LYS R 57 " --> pdb=" O HIS R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 77 removed outlier: 3.886A pdb=" N VAL R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL R 73 " --> pdb=" O SER R 69 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA R 74 " --> pdb=" O ASP R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 88 removed outlier: 3.845A pdb=" N LYS R 81 " --> pdb=" O VAL R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 127 removed outlier: 4.162A pdb=" N ILE R 98 " --> pdb=" O SER R 94 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA R 101 " --> pdb=" O ASN R 97 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER R 118 " --> pdb=" O LEU R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 135 removed outlier: 3.676A pdb=" N GLU R 132 " --> pdb=" O PRO R 128 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG R 133 " --> pdb=" O PHE R 129 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET R 135 " --> pdb=" O TYR R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 162 removed outlier: 4.784A pdb=" N ILE R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Proline residue: R 158 - end of helix Processing helix chain 'R' and resid 191 through 203 removed outlier: 3.599A pdb=" N ILE R 196 " --> pdb=" O ARG R 192 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 242 Processing helix chain 'R' and resid 265 through 298 removed outlier: 3.576A pdb=" N LEU R 274 " --> pdb=" O VAL R 270 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) Proline residue: R 287 - end of helix removed outlier: 4.145A pdb=" N LEU R 291 " --> pdb=" O PRO R 287 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS R 293 " --> pdb=" O PHE R 289 " (cutoff:3.500A) Proline residue: R 296 - end of helix Processing helix chain 'R' and resid 309 through 332 removed outlier: 3.648A pdb=" N TRP R 318 " --> pdb=" O ASP R 314 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE R 319 " --> pdb=" O VAL R 315 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN R 323 " --> pdb=" O PHE R 319 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER R 324 " --> pdb=" O GLY R 320 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER R 325 " --> pdb=" O TRP R 321 " (cutoff:3.500A) Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 334 through 346 Processing helix chain 'A' and resid 10 through 40 Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.580A pdb=" N GLN A 98 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS A 99 " --> pdb=" O TRP A 96 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN A 101 " --> pdb=" O GLN A 98 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP A 102 " --> pdb=" O CYS A 99 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 103 " --> pdb=" O PHE A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 145 through 154 removed outlier: 3.668A pdb=" N LEU A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 164 removed outlier: 4.155A pdb=" N ASP A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 183 through 205 removed outlier: 3.559A pdb=" N PHE A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.673A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.919A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 61 through 65 removed outlier: 3.527A pdb=" N VAL N 64 " --> pdb=" O THR N 61 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 removed outlier: 6.180A pdb=" N HIS A 41 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N PHE A 84 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU A 43 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL A 86 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU A 45 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA A 105 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.977A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.785A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.071A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.680A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.612A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.617A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.602A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.576A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.698A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 427 hydrogen bonds defined for protein. 1236 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: 2.57 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2114 1.33 - 1.45: 1750 1.45 - 1.58: 4760 1.58 - 1.70: 0 1.70 - 1.82: 78 Bond restraints: 8702 Sorted by residual: bond pdb=" C05 G4C R 502 " pdb=" N04 G4C R 502 " ideal model delta sigma weight residual 1.355 1.497 -0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" C03 G4C R 502 " pdb=" N04 G4C R 502 " ideal model delta sigma weight residual 1.460 1.497 -0.037 2.00e-02 2.50e+03 3.36e+00 bond pdb=" C ILE R 205 " pdb=" N PRO R 206 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.28e-02 6.10e+03 3.31e+00 bond pdb=" C MET R 78 " pdb=" N PRO R 79 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.30e-02 5.92e+03 3.19e+00 bond pdb=" C5 CLR R 505 " pdb=" C6 CLR R 505 " ideal model delta sigma weight residual 1.332 1.300 0.032 2.00e-02 2.50e+03 2.53e+00 ... (remaining 8697 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 11335 2.02 - 4.05: 409 4.05 - 6.07: 34 6.07 - 8.10: 13 8.10 - 10.12: 4 Bond angle restraints: 11795 Sorted by residual: angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 121.54 130.97 -9.43 1.91e+00 2.74e-01 2.44e+01 angle pdb=" C ILE R 294 " pdb=" N LEU R 295 " pdb=" CA LEU R 295 " ideal model delta sigma weight residual 121.62 127.01 -5.39 1.57e+00 4.06e-01 1.18e+01 angle pdb=" CA ASN B 119 " pdb=" CB ASN B 119 " pdb=" CG ASN B 119 " ideal model delta sigma weight residual 112.60 115.60 -3.00 1.00e+00 1.00e+00 8.97e+00 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 122.40 126.70 -4.30 1.45e+00 4.76e-01 8.78e+00 angle pdb=" N MET R 78 " pdb=" CA MET R 78 " pdb=" C MET R 78 " ideal model delta sigma weight residual 112.75 116.65 -3.90 1.36e+00 5.41e-01 8.23e+00 ... (remaining 11790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 5299 17.89 - 35.77: 119 35.77 - 53.65: 24 53.65 - 71.54: 1 71.54 - 89.42: 5 Dihedral angle restraints: 5448 sinusoidal: 2393 harmonic: 3055 Sorted by residual: dihedral pdb=" CB CYS R 298 " pdb=" SG CYS R 298 " pdb=" SG CYS R 307 " pdb=" CB CYS R 307 " ideal model delta sinusoidal sigma weight residual 93.00 -179.67 -87.33 1 1.00e+01 1.00e-02 9.15e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 166.82 -73.82 1 1.00e+01 1.00e-02 6.93e+01 dihedral pdb=" CA LEU B 198 " pdb=" C LEU B 198 " pdb=" N PHE B 199 " pdb=" CA PHE B 199 " ideal model delta harmonic sigma weight residual 180.00 159.61 20.39 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 5445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1173 0.082 - 0.163: 126 0.163 - 0.245: 19 0.245 - 0.327: 6 0.327 - 0.408: 5 Chirality restraints: 1329 Sorted by residual: chirality pdb=" C14 CLR R 507 " pdb=" C13 CLR R 507 " pdb=" C15 CLR R 507 " pdb=" C8 CLR R 507 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" C14 CLR R 504 " pdb=" C13 CLR R 504 " pdb=" C15 CLR R 504 " pdb=" C8 CLR R 504 " both_signs ideal model delta sigma weight residual False -2.32 -2.70 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" C14 CLR R 503 " pdb=" C13 CLR R 503 " pdb=" C15 CLR R 503 " pdb=" C8 CLR R 503 " both_signs ideal model delta sigma weight residual False -2.32 -2.70 0.39 2.00e-01 2.50e+01 3.73e+00 ... (remaining 1326 not shown) Planarity restraints: 1463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C03 G4C R 502 " -0.215 2.00e-02 2.50e+03 1.50e-01 3.37e+02 pdb=" C05 G4C R 502 " 0.047 2.00e-02 2.50e+03 pdb=" C06 G4C R 502 " -0.169 2.00e-02 2.50e+03 pdb=" C16 G4C R 502 " 0.029 2.00e-02 2.50e+03 pdb=" N04 G4C R 502 " 0.222 2.00e-02 2.50e+03 pdb=" O15 G4C R 502 " 0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 207 " 0.014 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" C VAL R 207 " -0.047 2.00e-02 2.50e+03 pdb=" O VAL R 207 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA R 208 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 93 " -0.035 5.00e-02 4.00e+02 5.38e-02 4.64e+00 pdb=" N PRO B 94 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 94 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 94 " -0.030 5.00e-02 4.00e+02 ... (remaining 1460 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 2234 2.82 - 3.34: 7304 3.34 - 3.86: 13145 3.86 - 4.38: 15218 4.38 - 4.90: 27054 Nonbonded interactions: 64955 Sorted by model distance: nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.294 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.309 3.040 nonbonded pdb=" OH TYR A 170 " pdb=" OD2 ASP A 195 " model vdw 2.322 3.040 nonbonded pdb=" OG1 THR N 104 " pdb=" OD1 ASP N 106 " model vdw 2.337 3.040 nonbonded pdb=" OG SER R 198 " pdb=" O2 LDP R 501 " model vdw 2.349 3.040 ... (remaining 64950 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.120 Find NCS groups from input model: 0.100 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 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 : 0.004 0.142 8702 Z= 0.260 Angle : 0.853 10.120 11795 Z= 0.463 Chirality : 0.062 0.408 1329 Planarity : 0.007 0.150 1463 Dihedral : 8.668 89.425 3452 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.23), residues: 1030 helix: -1.11 (0.24), residues: 402 sheet: -0.32 (0.34), residues: 218 loop : -2.18 (0.25), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 133 HIS 0.013 0.003 HIS A 209 PHE 0.032 0.002 PHE A 108 TYR 0.014 0.002 TYR A 243 ARG 0.007 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.975 Fit side-chains REVERT: R 35 LEU cc_start: 0.7128 (mt) cc_final: 0.6899 (mt) REVERT: R 57 LYS cc_start: 0.8100 (mmtp) cc_final: 0.7800 (mtmt) REVERT: R 193 THR cc_start: 0.8282 (t) cc_final: 0.8063 (m) REVERT: R 197 SER cc_start: 0.8489 (t) cc_final: 0.7878 (m) REVERT: A 124 ASP cc_start: 0.7061 (m-30) cc_final: 0.6732 (m-30) REVERT: A 237 ARG cc_start: 0.7324 (mtt-85) cc_final: 0.7064 (mtt90) REVERT: B 13 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7839 (pp30) REVERT: B 66 ASP cc_start: 0.7119 (p0) cc_final: 0.6493 (t0) REVERT: B 170 ASP cc_start: 0.8247 (t0) cc_final: 0.7929 (t0) REVERT: B 178 THR cc_start: 0.7687 (m) cc_final: 0.7237 (p) REVERT: G 21 MET cc_start: 0.7768 (mtt) cc_final: 0.7549 (ttp) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.2896 time to fit residues: 78.0572 Evaluate side-chains 137 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 41 ASN R 60 ASN R 113 ASN R 242 GLN R 323 ASN A 14 ASN A 82 HIS B 62 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 239 ASN B 268 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.179671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.133255 restraints weight = 8911.814| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.15 r_work: 0.3307 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8702 Z= 0.306 Angle : 0.647 7.996 11795 Z= 0.342 Chirality : 0.045 0.155 1329 Planarity : 0.005 0.047 1463 Dihedral : 6.582 85.963 1545 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.66 % Allowed : 6.22 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.25), residues: 1030 helix: 1.01 (0.25), residues: 414 sheet: -0.34 (0.34), residues: 227 loop : -1.53 (0.28), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 169 HIS 0.009 0.002 HIS A 209 PHE 0.026 0.002 PHE R 129 TYR 0.018 0.002 TYR B 59 ARG 0.004 0.001 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.923 Fit side-chains REVERT: R 150 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7524 (tt) REVERT: R 283 CYS cc_start: 0.7928 (t) cc_final: 0.7545 (m) REVERT: R 333 PHE cc_start: 0.6998 (OUTLIER) cc_final: 0.6059 (m-10) REVERT: A 25 MET cc_start: 0.6102 (mmp) cc_final: 0.5888 (mtp) REVERT: A 34 LYS cc_start: 0.8219 (ttmp) cc_final: 0.8001 (ttmp) REVERT: A 124 ASP cc_start: 0.7664 (m-30) cc_final: 0.7458 (m-30) REVERT: A 163 TYR cc_start: 0.7602 (m-80) cc_final: 0.7348 (m-80) REVERT: B 19 ARG cc_start: 0.6618 (mtp180) cc_final: 0.6371 (mmt90) REVERT: B 66 ASP cc_start: 0.7386 (p0) cc_final: 0.6978 (t0) REVERT: B 170 ASP cc_start: 0.8479 (t0) cc_final: 0.8251 (t0) REVERT: G 21 MET cc_start: 0.8341 (mtt) cc_final: 0.7600 (tmm) REVERT: N 25 SER cc_start: 0.8244 (t) cc_final: 0.7816 (p) outliers start: 15 outliers final: 7 residues processed: 151 average time/residue: 0.2149 time to fit residues: 44.2002 Evaluate side-chains 123 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 269 LYS Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 263 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 8 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 242 GLN R 323 ASN B 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.180353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.135044 restraints weight = 9001.642| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.93 r_work: 0.3344 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8702 Z= 0.179 Angle : 0.525 9.416 11795 Z= 0.277 Chirality : 0.041 0.144 1329 Planarity : 0.004 0.045 1463 Dihedral : 6.179 81.919 1545 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.77 % Allowed : 7.33 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.53 (0.26), residues: 1030 helix: 2.12 (0.25), residues: 401 sheet: -0.17 (0.34), residues: 225 loop : -1.17 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 133 HIS 0.008 0.001 HIS A 82 PHE 0.011 0.001 PHE A 74 TYR 0.009 0.001 TYR B 105 ARG 0.007 0.000 ARG R 226 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.910 Fit side-chains REVERT: R 233 ARG cc_start: 0.7118 (ttm110) cc_final: 0.6367 (mtp85) REVERT: R 283 CYS cc_start: 0.7847 (t) cc_final: 0.7606 (m) REVERT: A 124 ASP cc_start: 0.7561 (m-30) cc_final: 0.7341 (m-30) REVERT: B 66 ASP cc_start: 0.7190 (p0) cc_final: 0.6744 (t0) REVERT: B 111 TYR cc_start: 0.8981 (m-80) cc_final: 0.8728 (m-80) REVERT: G 21 MET cc_start: 0.8274 (mtt) cc_final: 0.7581 (tmm) REVERT: N 25 SER cc_start: 0.8250 (t) cc_final: 0.7965 (p) outliers start: 25 outliers final: 14 residues processed: 146 average time/residue: 0.2148 time to fit residues: 43.1658 Evaluate side-chains 121 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 24 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 32 optimal weight: 0.0370 chunk 26 optimal weight: 0.0980 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 13 optimal weight: 0.0050 chunk 41 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.3672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.184313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.142128 restraints weight = 8944.634| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.92 r_work: 0.3368 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8702 Z= 0.124 Angle : 0.482 7.047 11795 Z= 0.255 Chirality : 0.040 0.138 1329 Planarity : 0.003 0.047 1463 Dihedral : 5.783 79.898 1545 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.00 % Allowed : 8.99 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.93 (0.26), residues: 1030 helix: 2.59 (0.25), residues: 396 sheet: -0.10 (0.34), residues: 225 loop : -0.98 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS A 82 PHE 0.016 0.001 PHE A 192 TYR 0.016 0.001 TYR A 163 ARG 0.002 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: R 283 CYS cc_start: 0.7878 (t) cc_final: 0.7645 (m) REVERT: R 333 PHE cc_start: 0.6914 (OUTLIER) cc_final: 0.5753 (m-10) REVERT: A 34 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7806 (tttm) REVERT: A 124 ASP cc_start: 0.7631 (m-30) cc_final: 0.7415 (m-30) REVERT: A 163 TYR cc_start: 0.7886 (m-80) cc_final: 0.7567 (m-80) REVERT: A 242 GLN cc_start: 0.8103 (tt0) cc_final: 0.7654 (tt0) REVERT: B 66 ASP cc_start: 0.7146 (p0) cc_final: 0.6711 (t0) REVERT: B 111 TYR cc_start: 0.8880 (m-80) cc_final: 0.8569 (m-80) REVERT: G 21 MET cc_start: 0.8290 (mtt) cc_final: 0.7638 (tmm) outliers start: 18 outliers final: 12 residues processed: 134 average time/residue: 0.2099 time to fit residues: 39.0496 Evaluate side-chains 122 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 269 LYS Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 65 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 88 optimal weight: 0.1980 chunk 5 optimal weight: 0.8980 chunk 66 optimal weight: 0.0770 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.181728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.137878 restraints weight = 8883.080| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.95 r_work: 0.3323 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8702 Z= 0.152 Angle : 0.492 8.774 11795 Z= 0.256 Chirality : 0.040 0.135 1329 Planarity : 0.003 0.049 1463 Dihedral : 5.619 77.131 1545 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.22 % Allowed : 10.10 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.06 (0.26), residues: 1030 helix: 2.68 (0.25), residues: 396 sheet: -0.09 (0.33), residues: 231 loop : -0.85 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.005 0.001 HIS A 82 PHE 0.010 0.001 PHE A 74 TYR 0.012 0.001 TYR A 163 ARG 0.007 0.000 ARG R 226 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: R 85 GLU cc_start: 0.6728 (tp30) cc_final: 0.6243 (tp30) REVERT: R 283 CYS cc_start: 0.7833 (t) cc_final: 0.7618 (m) REVERT: R 333 PHE cc_start: 0.7031 (OUTLIER) cc_final: 0.5843 (m-10) REVERT: A 124 ASP cc_start: 0.7670 (m-30) cc_final: 0.7453 (m-30) REVERT: A 163 TYR cc_start: 0.7754 (m-80) cc_final: 0.7449 (m-80) REVERT: A 242 GLN cc_start: 0.8108 (tt0) cc_final: 0.7653 (tt0) REVERT: B 66 ASP cc_start: 0.7115 (p0) cc_final: 0.6699 (t0) REVERT: G 21 MET cc_start: 0.8271 (mtt) cc_final: 0.7549 (tmm) outliers start: 20 outliers final: 14 residues processed: 129 average time/residue: 0.2084 time to fit residues: 37.4292 Evaluate side-chains 123 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 43 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.180365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.136335 restraints weight = 8842.597| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.94 r_work: 0.3309 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8702 Z= 0.159 Angle : 0.492 8.390 11795 Z= 0.257 Chirality : 0.040 0.146 1329 Planarity : 0.003 0.051 1463 Dihedral : 5.493 73.511 1545 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.44 % Allowed : 9.99 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.08 (0.26), residues: 1030 helix: 2.70 (0.25), residues: 402 sheet: -0.11 (0.33), residues: 232 loop : -0.88 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS A 209 PHE 0.019 0.001 PHE A 192 TYR 0.010 0.001 TYR A 163 ARG 0.007 0.000 ARG R 226 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 1.415 Fit side-chains revert: symmetry clash REVERT: R 283 CYS cc_start: 0.7821 (t) cc_final: 0.7610 (m) REVERT: R 333 PHE cc_start: 0.7054 (OUTLIER) cc_final: 0.5931 (m-10) REVERT: A 40 THR cc_start: 0.7535 (OUTLIER) cc_final: 0.7270 (m) REVERT: A 124 ASP cc_start: 0.7666 (m-30) cc_final: 0.7457 (m-30) REVERT: A 163 TYR cc_start: 0.7739 (m-80) cc_final: 0.7463 (m-80) REVERT: A 242 GLN cc_start: 0.8068 (tt0) cc_final: 0.7600 (tt0) REVERT: A 244 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8288 (mm-30) REVERT: B 66 ASP cc_start: 0.7067 (p0) cc_final: 0.6678 (t0) REVERT: B 111 TYR cc_start: 0.8908 (m-80) cc_final: 0.8627 (m-80) REVERT: G 21 MET cc_start: 0.8291 (mtt) cc_final: 0.7640 (tmm) outliers start: 22 outliers final: 16 residues processed: 132 average time/residue: 0.2427 time to fit residues: 44.8163 Evaluate side-chains 125 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 30 optimal weight: 0.9980 chunk 77 optimal weight: 0.0000 chunk 36 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 63 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.181989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.138287 restraints weight = 8865.081| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.93 r_work: 0.3337 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8702 Z= 0.132 Angle : 0.493 9.170 11795 Z= 0.255 Chirality : 0.040 0.147 1329 Planarity : 0.003 0.051 1463 Dihedral : 5.378 71.647 1545 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.33 % Allowed : 10.65 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.23 (0.26), residues: 1030 helix: 2.91 (0.25), residues: 396 sheet: -0.09 (0.33), residues: 228 loop : -0.80 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS A 209 PHE 0.013 0.001 PHE A 192 TYR 0.009 0.001 TYR A 163 ARG 0.008 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: R 85 GLU cc_start: 0.6617 (tp30) cc_final: 0.5954 (mm-30) REVERT: R 283 CYS cc_start: 0.7883 (t) cc_final: 0.7601 (m) REVERT: R 333 PHE cc_start: 0.6928 (OUTLIER) cc_final: 0.5759 (m-10) REVERT: A 124 ASP cc_start: 0.7663 (m-30) cc_final: 0.7446 (m-30) REVERT: A 163 TYR cc_start: 0.7552 (m-80) cc_final: 0.7303 (m-80) REVERT: A 233 ASP cc_start: 0.8316 (m-30) cc_final: 0.8081 (m-30) REVERT: A 242 GLN cc_start: 0.8060 (tt0) cc_final: 0.7595 (tt0) REVERT: A 244 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8293 (mm-30) REVERT: B 66 ASP cc_start: 0.7067 (p0) cc_final: 0.6682 (t0) REVERT: B 111 TYR cc_start: 0.8879 (m-80) cc_final: 0.8592 (m-80) REVERT: G 21 MET cc_start: 0.8252 (mtt) cc_final: 0.7600 (tmm) outliers start: 21 outliers final: 18 residues processed: 136 average time/residue: 0.2247 time to fit residues: 42.1888 Evaluate side-chains 130 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 67 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 56 optimal weight: 0.3980 chunk 19 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.180381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.135676 restraints weight = 8976.553| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.96 r_work: 0.3314 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8702 Z= 0.149 Angle : 0.500 8.143 11795 Z= 0.259 Chirality : 0.040 0.161 1329 Planarity : 0.003 0.052 1463 Dihedral : 5.310 68.929 1545 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.55 % Allowed : 11.21 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.21 (0.26), residues: 1030 helix: 2.86 (0.25), residues: 401 sheet: -0.09 (0.32), residues: 228 loop : -0.82 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS A 209 PHE 0.022 0.001 PHE A 192 TYR 0.009 0.001 TYR B 105 ARG 0.007 0.000 ARG R 226 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: R 283 CYS cc_start: 0.7876 (t) cc_final: 0.7588 (m) REVERT: R 333 PHE cc_start: 0.6986 (OUTLIER) cc_final: 0.6034 (m-10) REVERT: A 40 THR cc_start: 0.7593 (OUTLIER) cc_final: 0.7340 (m) REVERT: A 124 ASP cc_start: 0.7670 (m-30) cc_final: 0.7446 (m-30) REVERT: A 163 TYR cc_start: 0.7558 (m-80) cc_final: 0.7307 (m-80) REVERT: A 202 THR cc_start: 0.6934 (m) cc_final: 0.6445 (p) REVERT: A 233 ASP cc_start: 0.8325 (m-30) cc_final: 0.8076 (m-30) REVERT: A 242 GLN cc_start: 0.8064 (tt0) cc_final: 0.7600 (tt0) REVERT: B 66 ASP cc_start: 0.7075 (p0) cc_final: 0.6637 (t0) REVERT: B 111 TYR cc_start: 0.8909 (m-80) cc_final: 0.8670 (m-80) REVERT: G 21 MET cc_start: 0.8217 (mtt) cc_final: 0.7581 (tmm) outliers start: 23 outliers final: 19 residues processed: 132 average time/residue: 0.2195 time to fit residues: 39.9994 Evaluate side-chains 128 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 31 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.179741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.136207 restraints weight = 8920.859| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.91 r_work: 0.3310 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8702 Z= 0.160 Angle : 0.511 7.399 11795 Z= 0.265 Chirality : 0.040 0.164 1329 Planarity : 0.003 0.052 1463 Dihedral : 5.291 66.184 1545 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.55 % Allowed : 11.43 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.20 (0.26), residues: 1030 helix: 2.82 (0.25), residues: 402 sheet: -0.07 (0.32), residues: 228 loop : -0.80 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS A 209 PHE 0.023 0.001 PHE A 192 TYR 0.008 0.001 TYR A 191 ARG 0.008 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: R 163 TRP cc_start: 0.5285 (m100) cc_final: 0.4392 (t60) REVERT: R 283 CYS cc_start: 0.7867 (t) cc_final: 0.7574 (m) REVERT: R 333 PHE cc_start: 0.7030 (OUTLIER) cc_final: 0.6233 (m-10) REVERT: A 40 THR cc_start: 0.7634 (OUTLIER) cc_final: 0.7374 (m) REVERT: A 124 ASP cc_start: 0.7653 (m-30) cc_final: 0.7435 (m-30) REVERT: A 163 TYR cc_start: 0.7724 (m-80) cc_final: 0.7427 (m-80) REVERT: A 202 THR cc_start: 0.6916 (m) cc_final: 0.6443 (p) REVERT: A 242 GLN cc_start: 0.8031 (tt0) cc_final: 0.7571 (tt0) REVERT: B 66 ASP cc_start: 0.7119 (p0) cc_final: 0.6735 (t0) REVERT: G 21 MET cc_start: 0.8181 (mtt) cc_final: 0.7551 (tmm) outliers start: 23 outliers final: 20 residues processed: 122 average time/residue: 0.2096 time to fit residues: 35.4708 Evaluate side-chains 124 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 7 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 23 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.179798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.136351 restraints weight = 8889.402| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.92 r_work: 0.3320 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 8702 Z= 0.153 Angle : 0.511 7.376 11795 Z= 0.264 Chirality : 0.040 0.160 1329 Planarity : 0.003 0.051 1463 Dihedral : 5.201 62.882 1545 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.66 % Allowed : 11.76 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.23 (0.26), residues: 1030 helix: 2.93 (0.25), residues: 396 sheet: -0.11 (0.32), residues: 228 loop : -0.78 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS A 209 PHE 0.024 0.001 PHE A 192 TYR 0.007 0.001 TYR A 163 ARG 0.008 0.000 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: R 163 TRP cc_start: 0.5369 (m100) cc_final: 0.4437 (t60) REVERT: R 283 CYS cc_start: 0.7838 (t) cc_final: 0.7622 (m) REVERT: R 333 PHE cc_start: 0.7014 (OUTLIER) cc_final: 0.6460 (m-10) REVERT: A 40 THR cc_start: 0.7621 (OUTLIER) cc_final: 0.7362 (m) REVERT: A 124 ASP cc_start: 0.7637 (m-30) cc_final: 0.7417 (m-30) REVERT: A 163 TYR cc_start: 0.7729 (m-80) cc_final: 0.7378 (m-80) REVERT: A 202 THR cc_start: 0.6957 (m) cc_final: 0.6486 (p) REVERT: A 233 ASP cc_start: 0.8313 (m-30) cc_final: 0.8075 (m-30) REVERT: A 242 GLN cc_start: 0.8119 (tt0) cc_final: 0.7669 (tt0) REVERT: B 66 ASP cc_start: 0.7118 (p0) cc_final: 0.6738 (t0) REVERT: G 21 MET cc_start: 0.8180 (mtt) cc_final: 0.7586 (tmm) outliers start: 24 outliers final: 19 residues processed: 122 average time/residue: 0.2032 time to fit residues: 34.7962 Evaluate side-chains 124 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 15 optimal weight: 7.9990 chunk 10 optimal weight: 0.0980 chunk 26 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.180301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.136992 restraints weight = 8952.853| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.94 r_work: 0.3320 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8702 Z= 0.148 Angle : 0.507 7.524 11795 Z= 0.263 Chirality : 0.040 0.163 1329 Planarity : 0.003 0.051 1463 Dihedral : 5.128 59.737 1545 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.55 % Allowed : 11.99 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.21 (0.26), residues: 1030 helix: 2.87 (0.25), residues: 402 sheet: -0.10 (0.32), residues: 226 loop : -0.82 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS A 209 PHE 0.023 0.001 PHE A 192 TYR 0.007 0.001 TYR A 191 ARG 0.008 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5702.71 seconds wall clock time: 99 minutes 45.05 seconds (5985.05 seconds total)