Starting phenix.real_space_refine on Thu Feb 13 09:44:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ljd_23391/02_2025/7ljd_23391.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ljd_23391/02_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_23391/02_2025/7ljd_23391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ljd_23391/02_2025/7ljd_23391.map" model { file = "/net/cci-nas-00/data/ceres_data/7ljd_23391/02_2025/7ljd_23391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ljd_23391/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.27, per 1000 atoms: 0.62 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: 2.14 Conformation dependent library (CDL) restraints added in 928.1 milliseconds 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: 0.92 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: 2.39 Time building geometry restraints manager: 2.46 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: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.570 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.220 ------------------------------------------------------------------------------- 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 : 0.845 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: 0.2913 time to fit residues: 77.9082 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 : 0.951 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.179822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.133528 restraints weight = 8906.703| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.12 r_work: 0.3310 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 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 = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 : 0.897 Fit side-chains REVERT: R 150 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7527 (tt) REVERT: R 283 CYS cc_start: 0.7934 (t) cc_final: 0.7554 (m) REVERT: R 333 PHE cc_start: 0.6998 (OUTLIER) cc_final: 0.6058 (m-10) REVERT: A 25 MET cc_start: 0.6101 (mmp) cc_final: 0.5889 (mtp) REVERT: A 34 LYS cc_start: 0.8222 (ttmp) cc_final: 0.8005 (ttmp) REVERT: A 124 ASP cc_start: 0.7665 (m-30) cc_final: 0.7457 (m-30) REVERT: A 163 TYR cc_start: 0.7596 (m-80) cc_final: 0.7342 (m-80) REVERT: B 19 ARG cc_start: 0.6606 (mtp180) cc_final: 0.6360 (mmt90) REVERT: B 66 ASP cc_start: 0.7382 (p0) cc_final: 0.6977 (t0) REVERT: B 170 ASP cc_start: 0.8485 (t0) cc_final: 0.8260 (t0) REVERT: G 21 MET cc_start: 0.8344 (mtt) cc_final: 0.7598 (tmm) REVERT: N 25 SER cc_start: 0.8243 (t) cc_final: 0.7815 (p) outliers start: 15 outliers final: 7 residues processed: 151 average time/residue: 0.2231 time to fit residues: 45.9838 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 : 0.958 ------------------------------------------------------------------------------- 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: 0.9980 chunk 58 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 0.1980 chunk 88 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 75 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 85 optimal weight: 9.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4017 r_free = 0.4017 target = 0.182901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.137965 restraints weight = 9003.412| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.92 r_work: 0.3365 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3348 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= 0.150 Angle : 0.511 9.346 11795 Z= 0.270 Chirality : 0.040 0.142 1329 Planarity : 0.003 0.045 1463 Dihedral : 6.116 82.673 1545 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.44 % Allowed : 7.66 % 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: 0.55 (0.26), residues: 1030 helix: 2.23 (0.25), residues: 396 sheet: -0.16 (0.33), residues: 225 loop : -1.21 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.007 0.001 HIS A 82 PHE 0.010 0.001 PHE B 199 TYR 0.010 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 153 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.965 Fit side-chains REVERT: R 233 ARG cc_start: 0.7088 (ttm110) cc_final: 0.6359 (mtp85) REVERT: R 283 CYS cc_start: 0.7839 (t) cc_final: 0.7604 (m) REVERT: A 124 ASP cc_start: 0.7551 (m-30) cc_final: 0.7328 (m-30) REVERT: B 66 ASP cc_start: 0.7291 (p0) cc_final: 0.6849 (t0) REVERT: B 111 TYR cc_start: 0.8974 (m-80) cc_final: 0.8743 (m-80) REVERT: B 214 ARG cc_start: 0.7330 (mpt180) cc_final: 0.7096 (mmt180) REVERT: G 21 MET cc_start: 0.8252 (mtt) cc_final: 0.7585 (tmm) REVERT: N 25 SER cc_start: 0.8229 (t) cc_final: 0.7946 (p) outliers start: 22 outliers final: 11 residues processed: 149 average time/residue: 0.2097 time to fit residues: 43.0297 Evaluate side-chains 124 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain B residue 43 ILE 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 20 LEU 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: 10.0000 chunk 80 optimal weight: 0.0670 chunk 32 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 5 optimal weight: 0.4980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.4017 r_free = 0.4017 target = 0.183345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.139618 restraints weight = 8912.548| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.97 r_work: 0.3351 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8702 Z= 0.138 Angle : 0.495 8.965 11795 Z= 0.260 Chirality : 0.040 0.140 1329 Planarity : 0.003 0.047 1463 Dihedral : 5.762 80.183 1545 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.22 % Allowed : 8.99 % Favored : 88.79 % 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: 0.94 (0.26), residues: 1030 helix: 2.61 (0.25), residues: 396 sheet: -0.06 (0.34), residues: 225 loop : -0.99 (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 209 PHE 0.017 0.001 PHE A 192 TYR 0.015 0.001 TYR A 163 ARG 0.003 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 140 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: R 76 LEU cc_start: 0.8025 (tt) cc_final: 0.7728 (tt) REVERT: R 283 CYS cc_start: 0.7884 (t) cc_final: 0.7645 (m) REVERT: A 34 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7833 (tttm) REVERT: A 124 ASP cc_start: 0.7555 (m-30) cc_final: 0.7343 (m-30) REVERT: A 163 TYR cc_start: 0.7807 (m-80) cc_final: 0.7538 (m-80) REVERT: A 242 GLN cc_start: 0.8142 (tt0) cc_final: 0.7692 (tt0) REVERT: B 66 ASP cc_start: 0.7155 (p0) cc_final: 0.6716 (t0) REVERT: B 111 TYR cc_start: 0.8889 (m-80) cc_final: 0.8571 (m-80) REVERT: B 214 ARG cc_start: 0.7419 (mpt180) cc_final: 0.7215 (mmt180) REVERT: G 21 MET cc_start: 0.8301 (mtt) cc_final: 0.7659 (tmm) outliers start: 20 outliers final: 15 residues processed: 135 average time/residue: 0.2148 time to fit residues: 40.0368 Evaluate side-chains 123 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 236 VAL Chi-restraints excluded: chain R residue 269 LYS Chi-restraints excluded: chain A residue 34 LYS 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 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 65 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 13 optimal weight: 0.0470 chunk 68 optimal weight: 5.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.182177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.138520 restraints weight = 8886.308| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.97 r_work: 0.3331 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 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 = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8702 Z= 0.145 Angle : 0.488 7.682 11795 Z= 0.255 Chirality : 0.040 0.143 1329 Planarity : 0.003 0.049 1463 Dihedral : 5.562 76.980 1545 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.66 % Allowed : 9.43 % Favored : 87.90 % 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: 1.01 (0.26), residues: 1030 helix: 2.61 (0.25), residues: 402 sheet: -0.05 (0.33), residues: 231 loop : -0.94 (0.29), residues: 397 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 0.010 0.001 TYR A 163 ARG 0.008 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 140 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: R 85 GLU cc_start: 0.6728 (tp30) cc_final: 0.6249 (tp30) REVERT: R 283 CYS cc_start: 0.7827 (t) cc_final: 0.7611 (m) REVERT: A 124 ASP cc_start: 0.7630 (m-30) cc_final: 0.7404 (m-30) REVERT: A 163 TYR cc_start: 0.7752 (m-80) cc_final: 0.7473 (m-80) REVERT: A 202 THR cc_start: 0.6872 (m) cc_final: 0.6371 (p) REVERT: A 242 GLN cc_start: 0.8094 (tt0) cc_final: 0.7651 (tt0) REVERT: B 66 ASP cc_start: 0.7138 (p0) cc_final: 0.6718 (t0) REVERT: B 111 TYR cc_start: 0.8891 (m-80) cc_final: 0.8608 (m-80) REVERT: G 21 MET cc_start: 0.8267 (mtt) cc_final: 0.7554 (tmm) outliers start: 24 outliers final: 18 residues processed: 134 average time/residue: 0.2146 time to fit residues: 39.7570 Evaluate side-chains 126 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 76 LEU 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 277 ILE Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain A residue 83 MET 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 43 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 58 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 72 optimal weight: 0.0070 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 = 0.4016 r_free = 0.4016 target = 0.183232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.139613 restraints weight = 8858.300| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.95 r_work: 0.3343 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.4056 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= 0.129 Angle : 0.475 7.583 11795 Z= 0.248 Chirality : 0.039 0.148 1329 Planarity : 0.003 0.049 1463 Dihedral : 5.350 74.758 1545 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.66 % Allowed : 9.54 % Favored : 87.79 % 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: 1.22 (0.26), residues: 1030 helix: 2.84 (0.25), residues: 396 sheet: 0.04 (0.33), residues: 230 loop : -0.82 (0.30), residues: 404 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 0.018 0.001 PHE A 192 TYR 0.010 0.001 TYR A 163 ARG 0.008 0.000 ARG B 197 *********************** 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 143 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 283 CYS cc_start: 0.7896 (t) cc_final: 0.7609 (m) REVERT: R 333 PHE cc_start: 0.7480 (OUTLIER) cc_final: 0.6625 (m-10) REVERT: A 124 ASP cc_start: 0.7623 (m-30) cc_final: 0.7404 (m-30) REVERT: A 163 TYR cc_start: 0.7708 (m-80) cc_final: 0.7444 (m-80) REVERT: A 242 GLN cc_start: 0.8122 (tt0) cc_final: 0.7680 (tt0) REVERT: B 66 ASP cc_start: 0.7103 (p0) cc_final: 0.6679 (t0) REVERT: B 111 TYR cc_start: 0.8866 (m-80) cc_final: 0.8586 (m-80) REVERT: B 214 ARG cc_start: 0.7585 (mpt180) cc_final: 0.7366 (mmt180) REVERT: G 21 MET cc_start: 0.8270 (mtt) cc_final: 0.7604 (tmm) outliers start: 24 outliers final: 22 residues processed: 134 average time/residue: 0.2029 time to fit residues: 38.2144 Evaluate side-chains 136 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 76 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 83 MET 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 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 ASN 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: 3.9990 chunk 36 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 24 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.179589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.133272 restraints weight = 8880.138| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.16 r_work: 0.3291 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8702 Z= 0.188 Angle : 0.523 9.299 11795 Z= 0.271 Chirality : 0.041 0.164 1329 Planarity : 0.003 0.051 1463 Dihedral : 5.472 71.727 1545 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.00 % Allowed : 9.43 % 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: 1.06 (0.26), residues: 1030 helix: 2.65 (0.25), residues: 407 sheet: -0.08 (0.32), residues: 235 loop : -0.94 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS A 82 PHE 0.015 0.001 PHE A 192 TYR 0.009 0.001 TYR N 94 ARG 0.007 0.000 ARG R 226 *********************** 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 151 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: R 283 CYS cc_start: 0.7788 (t) cc_final: 0.7566 (m) REVERT: R 333 PHE cc_start: 0.7560 (OUTLIER) cc_final: 0.6913 (m-10) REVERT: A 40 THR cc_start: 0.7673 (OUTLIER) cc_final: 0.7419 (m) REVERT: A 124 ASP cc_start: 0.7658 (m-30) cc_final: 0.7426 (m-30) REVERT: A 163 TYR cc_start: 0.7529 (m-80) cc_final: 0.7251 (m-80) REVERT: A 202 THR cc_start: 0.6983 (m) cc_final: 0.6508 (p) REVERT: A 242 GLN cc_start: 0.8099 (tt0) cc_final: 0.7646 (tt0) REVERT: B 66 ASP cc_start: 0.7094 (p0) cc_final: 0.6675 (t0) REVERT: B 111 TYR cc_start: 0.8914 (m-80) cc_final: 0.8705 (m-80) REVERT: G 21 MET cc_start: 0.8222 (mtt) cc_final: 0.7579 (tmm) outliers start: 27 outliers final: 20 residues processed: 141 average time/residue: 0.2262 time to fit residues: 43.7333 Evaluate side-chains 135 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 277 ILE 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 83 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 67 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 91 optimal weight: 0.0970 chunk 45 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3981 r_free = 0.3981 target = 0.179815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.136117 restraints weight = 8982.379| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.93 r_work: 0.3328 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 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 = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.4302 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= 0.158 Angle : 0.508 8.322 11795 Z= 0.264 Chirality : 0.040 0.156 1329 Planarity : 0.003 0.052 1463 Dihedral : 5.388 69.726 1545 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.66 % Allowed : 10.77 % Favored : 86.57 % 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: 1.20 (0.26), residues: 1030 helix: 2.83 (0.25), residues: 401 sheet: -0.05 (0.33), residues: 228 loop : -0.82 (0.30), residues: 401 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 0.017 0.001 PHE A 192 TYR 0.009 0.001 TYR B 105 ARG 0.008 0.000 ARG B 197 *********************** 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 141 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: R 283 CYS cc_start: 0.7807 (t) cc_final: 0.7601 (m) REVERT: R 333 PHE cc_start: 0.7556 (OUTLIER) cc_final: 0.6987 (m-10) REVERT: A 25 MET cc_start: 0.6177 (mmp) cc_final: 0.5962 (mtp) REVERT: A 124 ASP cc_start: 0.7668 (m-30) cc_final: 0.7455 (m-30) REVERT: A 163 TYR cc_start: 0.7571 (m-80) cc_final: 0.7310 (m-80) REVERT: A 202 THR cc_start: 0.6959 (m) cc_final: 0.6478 (p) REVERT: A 242 GLN cc_start: 0.8068 (tt0) cc_final: 0.7624 (tt0) REVERT: B 66 ASP cc_start: 0.7086 (p0) cc_final: 0.6655 (t0) REVERT: G 21 MET cc_start: 0.8223 (mtt) cc_final: 0.7569 (tmm) outliers start: 24 outliers final: 22 residues processed: 133 average time/residue: 0.2048 time to fit residues: 38.1107 Evaluate side-chains 131 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 71 GLU Chi-restraints excluded: chain A residue 83 MET 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 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: 0.8980 chunk 67 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 60 optimal weight: 0.0270 chunk 91 optimal weight: 0.4980 chunk 78 optimal weight: 0.8980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN 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 = 0.180280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.134465 restraints weight = 8934.603| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.97 r_work: 0.3322 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 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 = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 8702 Z= 0.150 Angle : 0.506 8.347 11795 Z= 0.263 Chirality : 0.040 0.162 1329 Planarity : 0.003 0.052 1463 Dihedral : 5.304 67.528 1545 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.66 % Allowed : 11.32 % 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: 1.24 (0.26), residues: 1030 helix: 2.85 (0.25), residues: 402 sheet: -0.03 (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 0.005 0.001 HIS A 209 PHE 0.026 0.001 PHE A 192 TYR 0.009 0.001 TYR B 105 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 130 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: R 163 TRP cc_start: 0.5251 (m100) cc_final: 0.4422 (t60) REVERT: R 283 CYS cc_start: 0.7862 (t) cc_final: 0.7575 (m) REVERT: R 333 PHE cc_start: 0.7558 (OUTLIER) cc_final: 0.7061 (m-10) REVERT: A 40 THR cc_start: 0.7579 (OUTLIER) cc_final: 0.7319 (m) REVERT: A 124 ASP cc_start: 0.7630 (m-30) cc_final: 0.7408 (m-30) REVERT: A 163 TYR cc_start: 0.7504 (m-80) cc_final: 0.7251 (m-80) REVERT: A 202 THR cc_start: 0.6899 (m) cc_final: 0.6434 (p) REVERT: A 242 GLN cc_start: 0.8065 (tt0) cc_final: 0.7616 (tt0) REVERT: B 66 ASP cc_start: 0.6992 (p0) cc_final: 0.6623 (t0) REVERT: G 21 MET cc_start: 0.8197 (mtt) cc_final: 0.7556 (tmm) outliers start: 24 outliers final: 22 residues processed: 123 average time/residue: 0.2228 time to fit residues: 37.6868 Evaluate side-chains 125 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 83 MET 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 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 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: 1.9990 chunk 36 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.179075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.132853 restraints weight = 8891.382| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.98 r_work: 0.3304 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8702 Z= 0.174 Angle : 0.521 7.655 11795 Z= 0.271 Chirality : 0.040 0.164 1329 Planarity : 0.003 0.052 1463 Dihedral : 5.303 63.763 1545 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.89 % Allowed : 11.43 % Favored : 85.68 % 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: 1.08 (0.26), residues: 1030 helix: 2.70 (0.25), residues: 408 sheet: -0.14 (0.32), residues: 226 loop : -0.90 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS A 209 PHE 0.016 0.001 PHE A 74 TYR 0.008 0.001 TYR A 191 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 132 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: R 163 TRP cc_start: 0.5366 (m100) cc_final: 0.4443 (t60) REVERT: R 333 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.7402 (m-10) REVERT: A 40 THR cc_start: 0.7755 (OUTLIER) cc_final: 0.7494 (m) REVERT: A 124 ASP cc_start: 0.7640 (m-30) cc_final: 0.7416 (m-30) REVERT: A 163 TYR cc_start: 0.7750 (m-80) cc_final: 0.7354 (m-80) REVERT: A 202 THR cc_start: 0.6970 (m) cc_final: 0.6518 (p) REVERT: A 242 GLN cc_start: 0.8131 (tt0) cc_final: 0.7695 (tt0) REVERT: B 66 ASP cc_start: 0.7082 (p0) cc_final: 0.6727 (t0) REVERT: B 97 SER cc_start: 0.8089 (p) cc_final: 0.7599 (t) REVERT: B 111 TYR cc_start: 0.8929 (m-80) cc_final: 0.8727 (m-80) REVERT: G 21 MET cc_start: 0.8157 (mtt) cc_final: 0.7549 (tmm) outliers start: 26 outliers final: 20 residues processed: 125 average time/residue: 0.2013 time to fit residues: 35.3331 Evaluate side-chains 125 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 83 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 15 optimal weight: 9.9990 chunk 10 optimal weight: 0.3980 chunk 26 optimal weight: 0.0070 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.181063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.137651 restraints weight = 8983.654| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.90 r_work: 0.3325 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8702 Z= 0.139 Angle : 0.498 7.500 11795 Z= 0.259 Chirality : 0.040 0.158 1329 Planarity : 0.003 0.051 1463 Dihedral : 5.158 61.123 1545 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.11 % Allowed : 12.76 % Favored : 85.13 % 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: 1.26 (0.26), residues: 1030 helix: 3.00 (0.25), residues: 396 sheet: -0.15 (0.32), residues: 226 loop : -0.79 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS A 209 PHE 0.015 0.001 PHE A 192 TYR 0.008 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: 5361.10 seconds wall clock time: 95 minutes 19.41 seconds (5719.41 seconds total)