Starting phenix.real_space_refine on Thu Mar 14 14:29:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wic_32528/03_2024/7wic_32528.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wic_32528/03_2024/7wic_32528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wic_32528/03_2024/7wic_32528.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wic_32528/03_2024/7wic_32528.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wic_32528/03_2024/7wic_32528.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wic_32528/03_2024/7wic_32528.pdb" } resolution = 2.8 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= 0.002 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 5769 2.51 5 N 1527 2.21 5 O 1682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9048 Number of models: 1 Model: "" Number of chains: 6 Chain: "L" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 114 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "R" Number of atoms: 2277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2277 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 11, 'TRANS': 276} Chain: "A" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1811 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "S" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1795 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Time building chain proxies: 4.56, per 1000 atoms: 0.50 Number of scatterers: 9048 At special positions: 0 Unit cell: (107.484, 127.764, 115.596, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 1682 8.00 N 1527 7.00 C 5769 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 3 " - pdb=" SG CYS L 14 " distance=2.03 Simple disulfide: pdb=" SG CYS R 115 " - pdb=" SG CYS R 193 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.4 seconds 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2162 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 37.5% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'R' and resid 41 through 69 removed outlier: 3.799A pdb=" N PHE R 48 " --> pdb=" O ALA R 44 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE R 49 " --> pdb=" O VAL R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 96 Processing helix chain 'R' and resid 97 through 105 removed outlier: 4.014A pdb=" N MET R 101 " --> pdb=" O PRO R 97 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN R 102 " --> pdb=" O PHE R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 146 removed outlier: 3.845A pdb=" N THR R 128 " --> pdb=" O ILE R 124 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS R 146 " --> pdb=" O LEU R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 154 removed outlier: 4.340A pdb=" N TRP R 153 " --> pdb=" O LYS R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 174 removed outlier: 3.638A pdb=" N ILE R 174 " --> pdb=" O SER R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 180 Processing helix chain 'R' and resid 202 through 243 removed outlier: 5.470A pdb=" N VAL R 219 " --> pdb=" O LEU R 215 " (cutoff:3.500A) Proline residue: R 220 - end of helix removed outlier: 3.592A pdb=" N VAL R 242 " --> pdb=" O SER R 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 246 through 282 Proline residue: R 271 - end of helix Processing helix chain 'R' and resid 287 through 313 removed outlier: 4.140A pdb=" N THR R 301 " --> pdb=" O VAL R 297 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR R 302 " --> pdb=" O VAL R 298 " (cutoff:3.500A) Proline residue: R 309 - end of helix Processing helix chain 'R' and resid 318 through 327 removed outlier: 4.267A pdb=" N SER R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.925A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 5.081A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.166A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.722A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 33 through 37 removed outlier: 4.174A pdb=" N ASN B 36 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.558A pdb=" N ALA G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.080A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.731A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.915A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 181 through 182 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.173A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.545A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.852A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.872A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.546A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.460A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.649A pdb=" N THR B 243 " --> pdb=" O ARG B 251 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.552A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.889A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA S 40 " --> pdb=" O GLY S 44 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY S 44 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.156A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 455 hydrogen bonds defined for protein. 1275 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: 2.73 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1461 1.30 - 1.43: 2445 1.43 - 1.56: 5229 1.56 - 1.69: 0 1.69 - 1.82: 102 Bond restraints: 9237 Sorted by residual: bond pdb=" CA VAL R 299 " pdb=" CB VAL R 299 " ideal model delta sigma weight residual 1.540 1.458 0.083 1.45e-02 4.76e+03 3.25e+01 bond pdb=" C ALA R 307 " pdb=" O ALA R 307 " ideal model delta sigma weight residual 1.236 1.169 0.067 1.29e-02 6.01e+03 2.70e+01 bond pdb=" C CYS R 306 " pdb=" O CYS R 306 " ideal model delta sigma weight residual 1.237 1.181 0.055 1.19e-02 7.06e+03 2.14e+01 bond pdb=" CB ASP R 122 " pdb=" CG ASP R 122 " ideal model delta sigma weight residual 1.516 1.404 0.112 2.50e-02 1.60e+03 2.01e+01 bond pdb=" N THR R 301 " pdb=" CA THR R 301 " ideal model delta sigma weight residual 1.459 1.407 0.052 1.21e-02 6.83e+03 1.84e+01 ... (remaining 9232 not shown) Histogram of bond angle deviations from ideal: 99.28 - 106.22: 183 106.22 - 113.16: 5000 113.16 - 120.10: 3196 120.10 - 127.05: 4023 127.05 - 133.99: 101 Bond angle restraints: 12503 Sorted by residual: angle pdb=" C ASP R 122 " pdb=" CA ASP R 122 " pdb=" CB ASP R 122 " ideal model delta sigma weight residual 110.88 102.64 8.24 1.57e+00 4.06e-01 2.76e+01 angle pdb=" N ASP R 122 " pdb=" CA ASP R 122 " pdb=" C ASP R 122 " ideal model delta sigma weight residual 111.07 115.70 -4.63 1.07e+00 8.73e-01 1.87e+01 angle pdb=" N THR R 120 " pdb=" CA THR R 120 " pdb=" C THR R 120 " ideal model delta sigma weight residual 111.28 115.54 -4.26 1.09e+00 8.42e-01 1.53e+01 angle pdb=" N CYS R 306 " pdb=" CA CYS R 306 " pdb=" C CYS R 306 " ideal model delta sigma weight residual 111.36 115.28 -3.92 1.09e+00 8.42e-01 1.29e+01 angle pdb=" CB MET A 240 " pdb=" CG MET A 240 " pdb=" SD MET A 240 " ideal model delta sigma weight residual 112.70 122.41 -9.71 3.00e+00 1.11e-01 1.05e+01 ... (remaining 12498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 4943 16.59 - 33.18: 440 33.18 - 49.77: 88 49.77 - 66.36: 9 66.36 - 82.95: 7 Dihedral angle restraints: 5487 sinusoidal: 2134 harmonic: 3353 Sorted by residual: dihedral pdb=" CB CYS L 3 " pdb=" SG CYS L 3 " pdb=" SG CYS L 14 " pdb=" CB CYS L 14 " ideal model delta sinusoidal sigma weight residual -86.00 -127.89 41.89 1 1.00e+01 1.00e-02 2.45e+01 dihedral pdb=" CB CYS R 115 " pdb=" SG CYS R 115 " pdb=" SG CYS R 193 " pdb=" CB CYS R 193 " ideal model delta sinusoidal sigma weight residual 93.00 130.96 -37.96 1 1.00e+01 1.00e-02 2.03e+01 dihedral pdb=" CA PHE A 323 " pdb=" C PHE A 323 " pdb=" N THR A 324 " pdb=" CA THR A 324 " ideal model delta harmonic sigma weight residual -180.00 -157.54 -22.46 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 5484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1310 0.085 - 0.170: 104 0.170 - 0.255: 6 0.255 - 0.340: 0 0.340 - 0.425: 1 Chirality restraints: 1421 Sorted by residual: chirality pdb=" CA THR R 120 " pdb=" N THR R 120 " pdb=" C THR R 120 " pdb=" CB THR R 120 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" CB VAL R 299 " pdb=" CA VAL R 299 " pdb=" CG1 VAL R 299 " pdb=" CG2 VAL R 299 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA THR R 301 " pdb=" N THR R 301 " pdb=" C THR R 301 " pdb=" CB THR R 301 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1418 not shown) Planarity restraints: 1571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 302 " 0.037 2.00e-02 2.50e+03 2.28e-02 1.04e+01 pdb=" CG TYR R 302 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR R 302 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR R 302 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR R 302 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR R 302 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR R 302 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR R 302 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS R 306 " -0.014 2.00e-02 2.50e+03 2.89e-02 8.34e+00 pdb=" C CYS R 306 " 0.050 2.00e-02 2.50e+03 pdb=" O CYS R 306 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA R 307 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 92 " -0.023 2.00e-02 2.50e+03 2.05e-02 7.36e+00 pdb=" CG PHE R 92 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE R 92 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE R 92 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE R 92 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE R 92 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE R 92 " -0.001 2.00e-02 2.50e+03 ... (remaining 1568 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 337 2.72 - 3.27: 8706 3.27 - 3.81: 14534 3.81 - 4.36: 17379 4.36 - 4.90: 30871 Nonbonded interactions: 71827 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.176 2.440 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.192 2.440 nonbonded pdb=" CB SER R 244 " pdb=" OE2 GLU A 318 " model vdw 2.194 3.440 nonbonded pdb=" O HIS R 146 " pdb=" OG SER R 150 " model vdw 2.232 2.440 nonbonded pdb=" OG1 THR A 182 " pdb=" N GLY A 183 " model vdw 2.273 2.520 ... (remaining 71822 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 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: 1.880 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 24.150 Find NCS groups from input model: 0.280 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: 0.010 Load rotamer database and sin/cos tables:11.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 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 : 0.005 0.112 9237 Z= 0.342 Angle : 0.620 9.737 12503 Z= 0.343 Chirality : 0.047 0.425 1421 Planarity : 0.004 0.038 1571 Dihedral : 12.934 82.950 3313 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.61 (0.25), residues: 1142 helix: 1.85 (0.27), residues: 393 sheet: 0.47 (0.31), residues: 300 loop : -0.94 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 269 HIS 0.002 0.001 HIS G 44 PHE 0.047 0.002 PHE R 92 TYR 0.052 0.002 TYR R 302 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 244 SER cc_start: 0.7953 (p) cc_final: 0.7625 (p) REVERT: A 29 LYS cc_start: 0.8167 (tmtt) cc_final: 0.7782 (tmtt) REVERT: A 231 ASP cc_start: 0.7026 (m-30) cc_final: 0.6711 (m-30) REVERT: A 237 ASP cc_start: 0.7227 (t0) cc_final: 0.6997 (t0) REVERT: A 262 THR cc_start: 0.8600 (m) cc_final: 0.8353 (t) REVERT: B 254 ASP cc_start: 0.7076 (t70) cc_final: 0.6787 (t70) REVERT: B 267 ASP cc_start: 0.7614 (m-30) cc_final: 0.7358 (m-30) REVERT: B 271 CYS cc_start: 0.7347 (p) cc_final: 0.7080 (p) REVERT: S 38 ARG cc_start: 0.7988 (ptt180) cc_final: 0.7742 (ptt180) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.9541 time to fit residues: 244.2587 Evaluate side-chains 216 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.0870 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 132 ASN B 220 GLN B 230 ASN B 340 ASN S 142 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9237 Z= 0.190 Angle : 0.530 11.213 12503 Z= 0.277 Chirality : 0.042 0.197 1421 Planarity : 0.004 0.034 1571 Dihedral : 4.123 21.624 1247 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.32 % Allowed : 9.67 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.91 (0.25), residues: 1142 helix: 2.24 (0.27), residues: 396 sheet: 0.57 (0.30), residues: 298 loop : -0.89 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 47 HIS 0.002 0.001 HIS R 107 PHE 0.042 0.002 PHE R 92 TYR 0.024 0.001 TYR S 190 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 219 time to evaluate : 0.996 Fit side-chains REVERT: R 116 ARG cc_start: 0.6793 (mtp180) cc_final: 0.6570 (mtp180) REVERT: R 174 ILE cc_start: 0.7613 (tp) cc_final: 0.7277 (pp) REVERT: A 29 LYS cc_start: 0.8145 (tmtt) cc_final: 0.7736 (tmtt) REVERT: A 231 ASP cc_start: 0.7031 (m-30) cc_final: 0.6714 (m-30) REVERT: B 45 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7647 (mtm) REVERT: B 66 ASP cc_start: 0.7496 (p0) cc_final: 0.7295 (p0) REVERT: B 243 THR cc_start: 0.8109 (p) cc_final: 0.7887 (p) REVERT: B 254 ASP cc_start: 0.6955 (t70) cc_final: 0.6742 (t70) REVERT: B 267 ASP cc_start: 0.7592 (m-30) cc_final: 0.7355 (m-30) REVERT: B 271 CYS cc_start: 0.7385 (p) cc_final: 0.7096 (p) REVERT: B 308 LEU cc_start: 0.8547 (mp) cc_final: 0.8333 (mp) REVERT: S 38 ARG cc_start: 0.7982 (ptt180) cc_final: 0.7777 (ptt180) outliers start: 23 outliers final: 12 residues processed: 224 average time/residue: 1.1109 time to fit residues: 265.7926 Evaluate side-chains 230 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 217 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 177 ILE Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 306 CYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 100 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 102 GLN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 132 ASN B 220 GLN B 230 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 9237 Z= 0.456 Angle : 0.650 15.362 12503 Z= 0.336 Chirality : 0.047 0.271 1421 Planarity : 0.004 0.035 1571 Dihedral : 4.481 23.150 1247 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.42 % Allowed : 12.89 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.59 (0.25), residues: 1142 helix: 1.90 (0.26), residues: 395 sheet: 0.44 (0.30), residues: 292 loop : -0.99 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP R 108 HIS 0.005 0.001 HIS S 35 PHE 0.045 0.002 PHE R 92 TYR 0.033 0.002 TYR S 190 ARG 0.004 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 235 time to evaluate : 0.935 Fit side-chains REVERT: R 174 ILE cc_start: 0.7873 (tp) cc_final: 0.7566 (pp) REVERT: A 29 LYS cc_start: 0.8140 (tmtt) cc_final: 0.7670 (tmtt) REVERT: A 231 ASP cc_start: 0.7051 (m-30) cc_final: 0.6737 (m-30) REVERT: B 45 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7643 (mtm) REVERT: B 66 ASP cc_start: 0.7511 (p0) cc_final: 0.7291 (p0) REVERT: B 127 LYS cc_start: 0.8612 (mtpp) cc_final: 0.8406 (mttt) REVERT: B 254 ASP cc_start: 0.7086 (t70) cc_final: 0.6878 (t70) REVERT: B 267 ASP cc_start: 0.7665 (m-30) cc_final: 0.7393 (m-30) REVERT: B 271 CYS cc_start: 0.7438 (p) cc_final: 0.7175 (p) REVERT: B 291 ASP cc_start: 0.7254 (p0) cc_final: 0.6969 (p0) REVERT: G 22 GLU cc_start: 0.7111 (tm-30) cc_final: 0.6857 (tm-30) REVERT: S 38 ARG cc_start: 0.7972 (ptt180) cc_final: 0.7733 (ptt180) REVERT: S 98 ARG cc_start: 0.8241 (ttt180) cc_final: 0.7979 (ttt180) outliers start: 34 outliers final: 22 residues processed: 244 average time/residue: 1.0196 time to fit residues: 267.4813 Evaluate side-chains 251 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 228 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 74 MET Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 128 THR Chi-restraints excluded: chain R residue 158 THR Chi-restraints excluded: chain R residue 238 SER Chi-restraints excluded: chain R residue 274 ILE Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain R residue 306 CYS Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 0.0980 chunk 108 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 304 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 132 ASN B 156 GLN B 176 GLN B 220 GLN B 230 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9237 Z= 0.182 Angle : 0.519 14.736 12503 Z= 0.270 Chirality : 0.042 0.196 1421 Planarity : 0.003 0.033 1571 Dihedral : 4.144 22.326 1247 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.63 % Allowed : 15.41 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.89 (0.25), residues: 1142 helix: 2.24 (0.27), residues: 397 sheet: 0.50 (0.29), residues: 301 loop : -0.87 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 108 HIS 0.003 0.001 HIS R 107 PHE 0.022 0.001 PHE R 92 TYR 0.025 0.001 TYR S 190 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 209 time to evaluate : 0.982 Fit side-chains REVERT: R 119 MET cc_start: 0.6596 (OUTLIER) cc_final: 0.6337 (mpp) REVERT: A 29 LYS cc_start: 0.8174 (tmtt) cc_final: 0.7856 (tttt) REVERT: A 33 GLU cc_start: 0.6789 (mt-10) cc_final: 0.6550 (tt0) REVERT: A 197 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7547 (ttmm) REVERT: A 231 ASP cc_start: 0.7021 (m-30) cc_final: 0.6724 (m-30) REVERT: A 243 MET cc_start: 0.8200 (tpp) cc_final: 0.6942 (mmm) REVERT: B 45 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7562 (mtm) REVERT: B 66 ASP cc_start: 0.7491 (p0) cc_final: 0.7283 (p0) REVERT: B 127 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8406 (mttt) REVERT: B 130 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6629 (pm20) REVERT: B 254 ASP cc_start: 0.6986 (t70) cc_final: 0.6772 (t70) REVERT: B 267 ASP cc_start: 0.7610 (m-30) cc_final: 0.7345 (m-30) REVERT: B 271 CYS cc_start: 0.7431 (p) cc_final: 0.7182 (p) outliers start: 36 outliers final: 19 residues processed: 218 average time/residue: 1.1463 time to fit residues: 267.3199 Evaluate side-chains 223 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 199 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 128 THR Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 284 ILE Chi-restraints excluded: chain R residue 287 THR Chi-restraints excluded: chain R residue 306 CYS Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 304 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 156 GLN B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 9237 Z= 0.530 Angle : 0.665 16.767 12503 Z= 0.345 Chirality : 0.048 0.267 1421 Planarity : 0.004 0.038 1571 Dihedral : 4.541 24.076 1247 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.14 % Allowed : 15.11 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.46 (0.25), residues: 1142 helix: 1.76 (0.26), residues: 395 sheet: 0.35 (0.29), residues: 292 loop : -1.03 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP R 108 HIS 0.006 0.002 HIS S 35 PHE 0.028 0.003 PHE R 92 TYR 0.031 0.002 TYR S 190 ARG 0.006 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 227 time to evaluate : 0.911 Fit side-chains REVERT: R 116 ARG cc_start: 0.6880 (mtp180) cc_final: 0.6566 (mtp180) REVERT: R 174 ILE cc_start: 0.7826 (tp) cc_final: 0.7555 (pp) REVERT: R 178 MET cc_start: 0.6904 (ttm) cc_final: 0.6518 (ttm) REVERT: R 212 THR cc_start: 0.7186 (t) cc_final: 0.6913 (m) REVERT: R 287 THR cc_start: 0.7019 (OUTLIER) cc_final: 0.6718 (m) REVERT: A 29 LYS cc_start: 0.8147 (tmtt) cc_final: 0.7799 (tttt) REVERT: A 231 ASP cc_start: 0.7070 (m-30) cc_final: 0.6735 (m-30) REVERT: B 45 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7672 (mtm) REVERT: B 254 ASP cc_start: 0.7089 (t70) cc_final: 0.6867 (t70) REVERT: B 267 ASP cc_start: 0.7669 (m-30) cc_final: 0.7385 (m-30) REVERT: B 271 CYS cc_start: 0.7453 (p) cc_final: 0.7213 (p) REVERT: B 291 ASP cc_start: 0.7320 (p0) cc_final: 0.7087 (p0) REVERT: G 22 GLU cc_start: 0.7060 (tm-30) cc_final: 0.6792 (tm-30) outliers start: 51 outliers final: 32 residues processed: 241 average time/residue: 0.9702 time to fit residues: 251.6986 Evaluate side-chains 256 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 222 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 74 MET Chi-restraints excluded: chain R residue 128 THR Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 274 ILE Chi-restraints excluded: chain R residue 278 SER Chi-restraints excluded: chain R residue 284 ILE Chi-restraints excluded: chain R residue 287 THR Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain R residue 306 CYS Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 304 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 156 GLN B 220 GLN B 230 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9237 Z= 0.199 Angle : 0.537 15.699 12503 Z= 0.276 Chirality : 0.043 0.200 1421 Planarity : 0.004 0.032 1571 Dihedral : 4.177 22.492 1247 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.53 % Allowed : 16.72 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.84 (0.25), residues: 1142 helix: 2.21 (0.27), residues: 395 sheet: 0.43 (0.29), residues: 300 loop : -0.87 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 108 HIS 0.004 0.001 HIS R 107 PHE 0.017 0.001 PHE R 92 TYR 0.025 0.001 TYR S 190 ARG 0.005 0.000 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 220 time to evaluate : 1.003 Fit side-chains REVERT: R 174 ILE cc_start: 0.7806 (tp) cc_final: 0.7485 (pp) REVERT: A 29 LYS cc_start: 0.8156 (tmtt) cc_final: 0.7833 (tttt) REVERT: A 231 ASP cc_start: 0.7016 (m-30) cc_final: 0.6706 (m-30) REVERT: A 240 MET cc_start: 0.7460 (tpp) cc_final: 0.7251 (tpp) REVERT: A 243 MET cc_start: 0.8224 (tpp) cc_final: 0.7346 (mmm) REVERT: B 45 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7583 (mtm) REVERT: B 130 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6624 (pm20) REVERT: B 254 ASP cc_start: 0.6997 (t70) cc_final: 0.6766 (t70) REVERT: B 267 ASP cc_start: 0.7611 (m-30) cc_final: 0.7337 (m-30) REVERT: B 271 CYS cc_start: 0.7448 (p) cc_final: 0.7154 (p) REVERT: S 38 ARG cc_start: 0.7861 (ptt180) cc_final: 0.7642 (ptt180) outliers start: 45 outliers final: 23 residues processed: 231 average time/residue: 1.0516 time to fit residues: 260.7097 Evaluate side-chains 243 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 218 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 74 MET Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 284 ILE Chi-restraints excluded: chain R residue 287 THR Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain R residue 306 CYS Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 304 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9237 Z= 0.269 Angle : 0.563 15.523 12503 Z= 0.289 Chirality : 0.043 0.226 1421 Planarity : 0.004 0.033 1571 Dihedral : 4.193 22.601 1247 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.73 % Allowed : 17.62 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.82 (0.25), residues: 1142 helix: 2.20 (0.27), residues: 395 sheet: 0.37 (0.28), residues: 301 loop : -0.83 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 269 HIS 0.004 0.001 HIS R 107 PHE 0.024 0.002 PHE R 92 TYR 0.027 0.002 TYR S 190 ARG 0.008 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 226 time to evaluate : 1.027 Fit side-chains REVERT: R 174 ILE cc_start: 0.7814 (tp) cc_final: 0.7506 (pp) REVERT: A 29 LYS cc_start: 0.8143 (tmtt) cc_final: 0.7805 (tttt) REVERT: A 231 ASP cc_start: 0.7017 (m-30) cc_final: 0.6699 (m-30) REVERT: A 243 MET cc_start: 0.8223 (tpp) cc_final: 0.7858 (mmm) REVERT: A 317 LYS cc_start: 0.8289 (ptpp) cc_final: 0.7835 (ptpt) REVERT: B 45 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7613 (mtm) REVERT: B 130 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6640 (pm20) REVERT: B 254 ASP cc_start: 0.7026 (t70) cc_final: 0.6810 (t70) REVERT: B 267 ASP cc_start: 0.7620 (m-30) cc_final: 0.7354 (m-30) REVERT: B 271 CYS cc_start: 0.7451 (p) cc_final: 0.7161 (p) REVERT: G 22 GLU cc_start: 0.7019 (tm-30) cc_final: 0.6783 (tm-30) outliers start: 37 outliers final: 26 residues processed: 236 average time/residue: 1.0370 time to fit residues: 262.9033 Evaluate side-chains 257 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 229 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 74 MET Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 284 ILE Chi-restraints excluded: chain R residue 287 THR Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain R residue 306 CYS Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 230 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9237 Z= 0.177 Angle : 0.523 14.806 12503 Z= 0.268 Chirality : 0.042 0.196 1421 Planarity : 0.003 0.032 1571 Dihedral : 4.040 21.399 1247 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.42 % Allowed : 18.83 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.25), residues: 1142 helix: 2.34 (0.27), residues: 396 sheet: 0.48 (0.29), residues: 296 loop : -0.80 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 269 HIS 0.004 0.001 HIS R 107 PHE 0.017 0.001 PHE R 92 TYR 0.023 0.001 TYR S 190 ARG 0.007 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 218 time to evaluate : 1.007 Fit side-chains REVERT: R 259 SER cc_start: 0.8086 (m) cc_final: 0.7754 (t) REVERT: A 29 LYS cc_start: 0.8140 (tmtt) cc_final: 0.7840 (tttt) REVERT: A 197 LYS cc_start: 0.7692 (ttmm) cc_final: 0.7480 (mtpp) REVERT: A 231 ASP cc_start: 0.7022 (m-30) cc_final: 0.6696 (m-30) REVERT: A 243 MET cc_start: 0.8230 (tpp) cc_final: 0.7883 (mmm) REVERT: A 317 LYS cc_start: 0.8248 (ptpp) cc_final: 0.7887 (ptpt) REVERT: B 45 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7579 (mtm) REVERT: B 130 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6704 (pm20) REVERT: B 214 ARG cc_start: 0.6805 (mtm-85) cc_final: 0.6603 (mtm-85) REVERT: B 267 ASP cc_start: 0.7587 (m-30) cc_final: 0.7312 (m-30) REVERT: B 271 CYS cc_start: 0.7445 (p) cc_final: 0.7159 (p) outliers start: 34 outliers final: 24 residues processed: 226 average time/residue: 1.0858 time to fit residues: 264.0646 Evaluate side-chains 242 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 216 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 74 MET Chi-restraints excluded: chain R residue 128 THR Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 287 THR Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain R residue 306 CYS Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9237 Z= 0.184 Angle : 0.537 14.503 12503 Z= 0.272 Chirality : 0.042 0.200 1421 Planarity : 0.003 0.031 1571 Dihedral : 4.021 20.831 1247 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.32 % Allowed : 19.74 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.25), residues: 1142 helix: 2.42 (0.27), residues: 397 sheet: 0.50 (0.29), residues: 291 loop : -0.79 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 269 HIS 0.011 0.001 HIS R 107 PHE 0.017 0.001 PHE R 92 TYR 0.023 0.001 TYR S 190 ARG 0.008 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 212 time to evaluate : 0.992 Fit side-chains REVERT: A 29 LYS cc_start: 0.8153 (tmtt) cc_final: 0.7851 (tttt) REVERT: A 231 ASP cc_start: 0.7028 (m-30) cc_final: 0.6699 (m-30) REVERT: A 243 MET cc_start: 0.8213 (tpp) cc_final: 0.7893 (mmm) REVERT: A 317 LYS cc_start: 0.8268 (ptpp) cc_final: 0.7911 (ptpt) REVERT: B 45 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7587 (mtm) REVERT: B 130 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6699 (pm20) REVERT: B 214 ARG cc_start: 0.6816 (mtm-85) cc_final: 0.6600 (mtm-85) REVERT: B 254 ASP cc_start: 0.7163 (t70) cc_final: 0.6960 (p0) REVERT: B 267 ASP cc_start: 0.7580 (m-30) cc_final: 0.7299 (m-30) REVERT: B 271 CYS cc_start: 0.7443 (p) cc_final: 0.7153 (p) outliers start: 33 outliers final: 23 residues processed: 221 average time/residue: 1.1114 time to fit residues: 262.7057 Evaluate side-chains 243 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 218 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 74 MET Chi-restraints excluded: chain R residue 128 THR Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 287 THR Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain R residue 306 CYS Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 0.0000 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9237 Z= 0.199 Angle : 0.537 14.371 12503 Z= 0.276 Chirality : 0.042 0.204 1421 Planarity : 0.004 0.041 1571 Dihedral : 4.038 20.744 1247 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.72 % Allowed : 20.44 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.04 (0.25), residues: 1142 helix: 2.42 (0.27), residues: 397 sheet: 0.52 (0.29), residues: 291 loop : -0.78 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 269 HIS 0.011 0.001 HIS R 107 PHE 0.018 0.001 PHE R 92 TYR 0.024 0.001 TYR S 190 ARG 0.006 0.000 ARG R 116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 218 time to evaluate : 0.968 Fit side-chains REVERT: R 119 MET cc_start: 0.6795 (mpp) cc_final: 0.6571 (mpm) REVERT: R 259 SER cc_start: 0.8118 (m) cc_final: 0.7793 (t) REVERT: A 29 LYS cc_start: 0.8174 (tmtt) cc_final: 0.7852 (tttt) REVERT: A 231 ASP cc_start: 0.7025 (m-30) cc_final: 0.6704 (m-30) REVERT: A 243 MET cc_start: 0.8190 (tpp) cc_final: 0.7867 (mmm) REVERT: A 317 LYS cc_start: 0.8247 (ptpp) cc_final: 0.7861 (ptmt) REVERT: B 45 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7608 (mtm) REVERT: B 130 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6701 (pm20) REVERT: B 214 ARG cc_start: 0.6815 (mtm-85) cc_final: 0.6604 (mtm-85) REVERT: B 254 ASP cc_start: 0.7258 (t70) cc_final: 0.7048 (p0) REVERT: B 267 ASP cc_start: 0.7576 (m-30) cc_final: 0.7304 (m-30) REVERT: B 271 CYS cc_start: 0.7435 (p) cc_final: 0.7195 (p) REVERT: S 215 THR cc_start: 0.8259 (m) cc_final: 0.7709 (p) outliers start: 27 outliers final: 24 residues processed: 224 average time/residue: 1.0881 time to fit residues: 261.1248 Evaluate side-chains 240 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 214 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 74 MET Chi-restraints excluded: chain R residue 128 THR Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 287 THR Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain R residue 306 CYS Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.140134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.119737 restraints weight = 11961.364| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.09 r_work: 0.3453 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9237 Z= 0.201 Angle : 0.554 14.299 12503 Z= 0.281 Chirality : 0.043 0.204 1421 Planarity : 0.003 0.033 1571 Dihedral : 4.032 20.679 1247 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.92 % Allowed : 20.85 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.07 (0.25), residues: 1142 helix: 2.46 (0.27), residues: 397 sheet: 0.56 (0.30), residues: 285 loop : -0.77 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 269 HIS 0.010 0.001 HIS R 107 PHE 0.016 0.001 PHE R 92 TYR 0.024 0.001 TYR S 190 ARG 0.007 0.000 ARG R 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4286.34 seconds wall clock time: 75 minutes 53.09 seconds (4553.09 seconds total)