Starting phenix.real_space_refine on Tue Sep 24 21:34:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljd_23391/09_2024/7ljd_23391.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljd_23391/09_2024/7ljd_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljd_23391/09_2024/7ljd_23391.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljd_23391/09_2024/7ljd_23391.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljd_23391/09_2024/7ljd_23391.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljd_23391/09_2024/7ljd_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 5.21, per 1000 atoms: 0.61 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: 2.03 Conformation dependent library (CDL) restraints added in 926.2 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: 1.01 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: 2.15 Time building geometry restraints manager: 2.37 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: 0.410 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: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.230 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.880 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 0.940 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: 0.2716 time to fit residues: 72.9817 Evaluate side-chains 137 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 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 fitting. rotamer outliers: 15 poor density : 141 time to evaluate : 0.946 Fit side-chains REVERT: R 150 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7298 (tt) REVERT: R 333 PHE cc_start: 0.7023 (OUTLIER) cc_final: 0.6099 (m-10) REVERT: A 34 LYS cc_start: 0.8042 (ttmp) cc_final: 0.7786 (ttmp) REVERT: A 83 MET cc_start: 0.8418 (ttp) cc_final: 0.8210 (ttm) REVERT: A 124 ASP cc_start: 0.6880 (m-30) cc_final: 0.6665 (m-30) REVERT: B 66 ASP cc_start: 0.7019 (p0) cc_final: 0.6767 (t0) REVERT: G 21 MET cc_start: 0.7995 (mtt) cc_final: 0.7575 (tmm) REVERT: N 25 SER cc_start: 0.8260 (t) cc_final: 0.7827 (p) outliers start: 15 outliers final: 7 residues processed: 151 average time/residue: 0.2175 time to fit residues: 44.5849 Evaluate side-chains 122 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 113 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 50 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 0.1980 chunk 31 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8702 Z= 0.158 Angle : 0.517 9.326 11795 Z= 0.274 Chirality : 0.041 0.144 1329 Planarity : 0.003 0.045 1463 Dihedral : 6.125 82.316 1545 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.33 % Allowed : 7.66 % Favored : 90.01 % 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: 0.54 (0.26), residues: 1030 helix: 2.10 (0.25), residues: 402 sheet: -0.15 (0.34), residues: 225 loop : -1.15 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.008 0.001 HIS A 82 PHE 0.010 0.001 PHE R 141 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 147 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 0.950 Fit side-chains REVERT: R 233 ARG cc_start: 0.6837 (ttm110) cc_final: 0.6120 (mtp85) REVERT: A 124 ASP cc_start: 0.6810 (m-30) cc_final: 0.6584 (m-30) REVERT: A 163 TYR cc_start: 0.7823 (m-80) cc_final: 0.7523 (m-80) REVERT: B 66 ASP cc_start: 0.6962 (p0) cc_final: 0.6677 (t0) REVERT: B 78 LYS cc_start: 0.8717 (tppt) cc_final: 0.8509 (tppp) REVERT: B 111 TYR cc_start: 0.8621 (m-80) cc_final: 0.8369 (m-80) REVERT: G 21 MET cc_start: 0.7949 (mtt) cc_final: 0.7560 (tmm) REVERT: N 25 SER cc_start: 0.8213 (t) cc_final: 0.7927 (p) outliers start: 21 outliers final: 13 residues processed: 144 average time/residue: 0.2062 time to fit residues: 41.0963 Evaluate side-chains 122 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 277 ILE 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 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 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 69 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 97 optimal weight: 0.2980 chunk 48 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8702 Z= 0.191 Angle : 0.524 9.042 11795 Z= 0.276 Chirality : 0.041 0.138 1329 Planarity : 0.003 0.049 1463 Dihedral : 5.972 78.970 1545 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.89 % Allowed : 8.32 % 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: 0.66 (0.26), residues: 1030 helix: 2.21 (0.25), residues: 408 sheet: -0.13 (0.34), residues: 225 loop : -1.12 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.006 0.001 HIS A 82 PHE 0.017 0.001 PHE A 192 TYR 0.010 0.001 TYR A 191 ARG 0.005 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 fitting. rotamer outliers: 26 poor density : 112 time to evaluate : 0.940 Fit side-chains REVERT: R 76 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7825 (tt) REVERT: R 160 GLN cc_start: 0.6089 (mm-40) cc_final: 0.5879 (mm-40) REVERT: A 124 ASP cc_start: 0.6812 (m-30) cc_final: 0.6580 (m-30) REVERT: A 202 THR cc_start: 0.6673 (m) cc_final: 0.6337 (p) REVERT: A 242 GLN cc_start: 0.7508 (tt0) cc_final: 0.7035 (tt0) REVERT: B 66 ASP cc_start: 0.6815 (p0) cc_final: 0.6546 (t0) REVERT: B 111 TYR cc_start: 0.8601 (m-80) cc_final: 0.8322 (m-80) REVERT: G 21 MET cc_start: 0.7966 (mtt) cc_final: 0.7640 (tmm) outliers start: 26 outliers final: 19 residues processed: 131 average time/residue: 0.1913 time to fit residues: 35.3998 Evaluate side-chains 125 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 132 GLU 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 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 A residue 152 LYS Chi-restraints excluded: chain B residue 43 ILE 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 N residue 20 LEU 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 55 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 67 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 24 optimal weight: 0.4980 chunk 32 optimal weight: 0.0270 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.4033 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= 0.154 Angle : 0.496 8.820 11795 Z= 0.260 Chirality : 0.040 0.139 1329 Planarity : 0.003 0.050 1463 Dihedral : 5.725 75.549 1545 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.77 % Allowed : 8.99 % Favored : 88.24 % 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: 0.96 (0.26), residues: 1030 helix: 2.57 (0.26), residues: 396 sheet: -0.13 (0.33), residues: 232 loop : -0.88 (0.30), residues: 402 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 B 241 TYR 0.024 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 136 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: R 85 GLU cc_start: 0.6199 (tp30) cc_final: 0.5872 (tp30) REVERT: R 333 PHE cc_start: 0.7467 (OUTLIER) cc_final: 0.6562 (m-10) REVERT: A 40 THR cc_start: 0.7468 (OUTLIER) cc_final: 0.7113 (m) REVERT: A 124 ASP cc_start: 0.6890 (m-30) cc_final: 0.6666 (m-30) REVERT: A 202 THR cc_start: 0.6607 (m) cc_final: 0.6322 (p) REVERT: A 242 GLN cc_start: 0.7506 (tt0) cc_final: 0.7038 (tt0) REVERT: B 66 ASP cc_start: 0.6740 (p0) cc_final: 0.6503 (t0) REVERT: B 111 TYR cc_start: 0.8572 (m-80) cc_final: 0.8274 (m-80) REVERT: B 195 ASP cc_start: 0.8209 (t0) cc_final: 0.8004 (t0) REVERT: B 197 ARG cc_start: 0.8471 (ttm110) cc_final: 0.8207 (mtp85) REVERT: G 21 MET cc_start: 0.7940 (mtt) cc_final: 0.7548 (tmm) outliers start: 25 outliers final: 19 residues processed: 128 average time/residue: 0.2030 time to fit residues: 36.5677 Evaluate side-chains 124 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 103 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 271 LEU 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 43 ILE 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 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 87 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 24 optimal weight: 0.0870 chunk 97 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 94 optimal weight: 2.9990 overall best weight: 2.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8702 Z= 0.341 Angle : 0.631 9.660 11795 Z= 0.329 Chirality : 0.044 0.174 1329 Planarity : 0.004 0.054 1463 Dihedral : 6.363 69.025 1545 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.66 % Allowed : 9.21 % Favored : 87.13 % 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: 0.50 (0.26), residues: 1030 helix: 2.00 (0.25), residues: 405 sheet: -0.25 (0.34), residues: 216 loop : -1.05 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.008 0.002 HIS A 82 PHE 0.021 0.002 PHE A 81 TYR 0.016 0.002 TYR N 94 ARG 0.010 0.001 ARG A 237 *********************** 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 145 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 112 time to evaluate : 0.962 Fit side-chains REVERT: R 50 ARG cc_start: 0.7192 (mtt-85) cc_final: 0.6955 (ttm-80) REVERT: R 163 TRP cc_start: 0.5149 (m100) cc_final: 0.4435 (t60) REVERT: A 40 THR cc_start: 0.8286 (OUTLIER) cc_final: 0.7965 (m) REVERT: A 124 ASP cc_start: 0.6867 (m-30) cc_final: 0.6616 (m-30) REVERT: A 202 THR cc_start: 0.6831 (m) cc_final: 0.6623 (p) REVERT: B 66 ASP cc_start: 0.6547 (p0) cc_final: 0.6315 (t0) REVERT: B 153 ASP cc_start: 0.7872 (p0) cc_final: 0.7600 (p0) REVERT: B 156 GLN cc_start: 0.7842 (mt0) cc_final: 0.7298 (mp10) REVERT: B 197 ARG cc_start: 0.8507 (ttm110) cc_final: 0.8234 (mtp85) REVERT: B 234 PHE cc_start: 0.9071 (OUTLIER) cc_final: 0.8828 (m-80) REVERT: G 21 MET cc_start: 0.7878 (mtt) cc_final: 0.7618 (tmm) outliers start: 33 outliers final: 25 residues processed: 133 average time/residue: 0.2119 time to fit residues: 38.4905 Evaluate side-chains 132 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 105 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 132 GLU 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 271 LEU Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 325 SER 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 152 LYS Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 119 ASN 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 20 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 60 optimal weight: 0.1980 chunk 59 optimal weight: 0.5980 chunk 44 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8702 Z= 0.147 Angle : 0.503 7.598 11795 Z= 0.266 Chirality : 0.040 0.139 1329 Planarity : 0.003 0.052 1463 Dihedral : 5.911 66.209 1545 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.22 % Allowed : 10.77 % 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: 0.92 (0.27), residues: 1030 helix: 2.56 (0.25), residues: 396 sheet: -0.27 (0.33), residues: 228 loop : -0.84 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS A 209 PHE 0.012 0.001 PHE N 108 TYR 0.019 0.001 TYR A 163 ARG 0.006 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 134 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 114 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: R 85 GLU cc_start: 0.6163 (tp30) cc_final: 0.5597 (mm-30) REVERT: R 163 TRP cc_start: 0.5194 (m100) cc_final: 0.4400 (t60) REVERT: R 283 CYS cc_start: 0.6443 (m) cc_final: 0.6155 (m) REVERT: A 124 ASP cc_start: 0.6894 (m-30) cc_final: 0.6650 (m-30) REVERT: A 233 ASP cc_start: 0.7589 (m-30) cc_final: 0.7300 (m-30) REVERT: B 97 SER cc_start: 0.7855 (p) cc_final: 0.7418 (t) REVERT: B 195 ASP cc_start: 0.8257 (t0) cc_final: 0.8052 (t0) REVERT: B 197 ARG cc_start: 0.8464 (ttm110) cc_final: 0.8257 (mtp85) REVERT: G 21 MET cc_start: 0.7860 (mtt) cc_final: 0.7609 (tmm) outliers start: 20 outliers final: 15 residues processed: 128 average time/residue: 0.2119 time to fit residues: 37.2500 Evaluate side-chains 119 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 75 VAL 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 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 A residue 221 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 160 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 88 optimal weight: 0.0470 chunk 93 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.6482 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.4608 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= 0.151 Angle : 0.517 9.277 11795 Z= 0.271 Chirality : 0.040 0.143 1329 Planarity : 0.003 0.053 1463 Dihedral : 5.708 64.711 1545 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.22 % Allowed : 11.32 % Favored : 86.46 % 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: 1.02 (0.27), residues: 1030 helix: 2.68 (0.25), residues: 395 sheet: -0.18 (0.33), residues: 228 loop : -0.84 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.005 0.001 HIS A 209 PHE 0.022 0.001 PHE A 192 TYR 0.020 0.001 TYR A 163 ARG 0.003 0.000 ARG A 237 *********************** 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 126 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 163 TRP cc_start: 0.5227 (m100) cc_final: 0.4395 (t60) REVERT: R 283 CYS cc_start: 0.6580 (m) cc_final: 0.6262 (m) REVERT: A 124 ASP cc_start: 0.6883 (m-30) cc_final: 0.6636 (m-30) REVERT: A 233 ASP cc_start: 0.7595 (m-30) cc_final: 0.7309 (m-30) REVERT: B 97 SER cc_start: 0.7848 (p) cc_final: 0.7426 (t) REVERT: B 197 ARG cc_start: 0.8474 (ttm110) cc_final: 0.8228 (mtp85) REVERT: G 21 MET cc_start: 0.7856 (mtt) cc_final: 0.7613 (tmm) outliers start: 20 outliers final: 19 residues processed: 121 average time/residue: 0.2043 time to fit residues: 34.6411 Evaluate side-chains 119 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 75 VAL 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 110 VAL Chi-restraints excluded: chain A residue 118 LEU 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 20 LEU 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 90 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 81 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8702 Z= 0.198 Angle : 0.536 8.810 11795 Z= 0.282 Chirality : 0.041 0.160 1329 Planarity : 0.004 0.053 1463 Dihedral : 5.585 60.838 1545 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.22 % Allowed : 11.65 % Favored : 86.13 % 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: 0.94 (0.26), residues: 1030 helix: 2.61 (0.25), residues: 401 sheet: -0.27 (0.33), residues: 228 loop : -0.90 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS A 209 PHE 0.024 0.001 PHE A 192 TYR 0.020 0.001 TYR A 163 ARG 0.008 0.000 ARG R 226 *********************** 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 128 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: R 85 GLU cc_start: 0.6182 (tp30) cc_final: 0.5657 (mm-30) REVERT: R 163 TRP cc_start: 0.5049 (m100) cc_final: 0.4573 (t60) REVERT: A 40 THR cc_start: 0.7961 (OUTLIER) cc_final: 0.7670 (m) REVERT: A 124 ASP cc_start: 0.6896 (m-30) cc_final: 0.6646 (m-30) REVERT: A 202 THR cc_start: 0.6739 (m) cc_final: 0.6498 (p) REVERT: B 97 SER cc_start: 0.7935 (p) cc_final: 0.7547 (t) REVERT: G 21 MET cc_start: 0.7827 (mtt) cc_final: 0.7598 (tmm) outliers start: 20 outliers final: 18 residues processed: 124 average time/residue: 0.2106 time to fit residues: 36.2597 Evaluate side-chains 123 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 75 VAL 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 40 THR 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 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 20 LEU 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 45 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 92 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 49 optimal weight: 0.2980 chunk 63 optimal weight: 0.0170 chunk 85 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.8620 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8702 Z= 0.167 Angle : 0.525 9.049 11795 Z= 0.275 Chirality : 0.041 0.156 1329 Planarity : 0.003 0.054 1463 Dihedral : 5.401 57.584 1545 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.11 % Allowed : 11.99 % Favored : 85.90 % 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: 0.97 (0.27), residues: 1030 helix: 2.69 (0.25), residues: 397 sheet: -0.27 (0.33), residues: 226 loop : -0.89 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.005 0.001 HIS A 209 PHE 0.025 0.001 PHE A 192 TYR 0.017 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 122 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: R 85 GLU cc_start: 0.6075 (tp30) cc_final: 0.5630 (mm-30) REVERT: R 163 TRP cc_start: 0.5191 (m100) cc_final: 0.4609 (t60) REVERT: A 40 THR cc_start: 0.7900 (OUTLIER) cc_final: 0.7594 (m) REVERT: A 124 ASP cc_start: 0.6893 (m-30) cc_final: 0.6647 (m-30) REVERT: A 233 ASP cc_start: 0.7584 (m-30) cc_final: 0.7290 (m-30) REVERT: B 97 SER cc_start: 0.7795 (p) cc_final: 0.7395 (t) REVERT: B 214 ARG cc_start: 0.7341 (mpt180) cc_final: 0.7083 (mmt180) REVERT: G 21 MET cc_start: 0.7815 (mtt) cc_final: 0.7582 (tmm) REVERT: N 110 VAL cc_start: 0.7805 (t) cc_final: 0.7428 (p) outliers start: 19 outliers final: 18 residues processed: 119 average time/residue: 0.2085 time to fit residues: 34.4340 Evaluate side-chains 120 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 75 VAL 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 40 THR 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 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 20 LEU 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 73 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 0.0770 chunk 82 optimal weight: 0.0270 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.179817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.134508 restraints weight = 8829.178| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.94 r_work: 0.3324 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- 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 = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8702 Z= 0.139 Angle : 0.502 8.495 11795 Z= 0.263 Chirality : 0.040 0.147 1329 Planarity : 0.004 0.054 1463 Dihedral : 5.115 53.932 1545 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.66 % Allowed : 12.87 % 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: 1.09 (0.27), residues: 1030 helix: 2.87 (0.25), residues: 396 sheet: -0.23 (0.33), residues: 226 loop : -0.90 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS A 209 PHE 0.025 0.001 PHE A 192 TYR 0.010 0.001 TYR B 105 ARG 0.008 0.000 ARG R 226 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2170.90 seconds wall clock time: 39 minutes 36.17 seconds (2376.17 seconds total)