Starting phenix.real_space_refine on Tue Nov 14 16:48:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wic_32528/11_2023/7wic_32528.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wic_32528/11_2023/7wic_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_32528/11_2023/7wic_32528.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wic_32528/11_2023/7wic_32528.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wic_32528/11_2023/7wic_32528.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wic_32528/11_2023/7wic_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-1.21rc1-5144/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: 4.93, per 1000 atoms: 0.54 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: 3.28 Conformation dependent library (CDL) restraints added in 1.7 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: 1.03 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: 2.83 Time building geometry restraints manager: 3.58 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: 0.350 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: 2.000 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.460 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.900 ------------------------------------------------------------------------------- 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 *********************** 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 : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.9893 time to fit residues: 252.8778 Evaluate side-chains 215 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.031 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5015 ------------------------------------------------------------------------------- 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: 2.9990 chunk 28 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 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: 0.8960 ------------------------------------------------------------------------------- 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: 0.7284 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9237 Z= 0.220 Angle : 0.548 11.177 12503 Z= 0.287 Chirality : 0.042 0.207 1421 Planarity : 0.004 0.034 1571 Dihedral : 4.185 22.173 1247 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.52 % Allowed : 10.17 % Favored : 87.31 % 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: 0.85 (0.25), residues: 1142 helix: 2.17 (0.27), residues: 396 sheet: 0.57 (0.30), residues: 299 loop : -0.91 (0.28), residues: 447 *********************** 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 243 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 218 time to evaluate : 0.969 Fit side-chains outliers start: 25 outliers final: 13 residues processed: 224 average time/residue: 1.1353 time to fit residues: 272.0801 Evaluate side-chains 230 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 217 time to evaluate : 1.038 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 4 residues processed: 10 average time/residue: 0.4694 time to fit residues: 6.7640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 0.0070 chunk 69 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.6004 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9237 Z= 0.322 Angle : 0.586 13.881 12503 Z= 0.304 Chirality : 0.044 0.242 1421 Planarity : 0.004 0.031 1571 Dihedral : 4.290 23.048 1247 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.42 % Allowed : 13.29 % Favored : 84.29 % 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: 0.80 (0.25), residues: 1142 helix: 2.17 (0.27), residues: 395 sheet: 0.49 (0.29), residues: 302 loop : -0.95 (0.28), residues: 445 *********************** 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 247 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 223 time to evaluate : 1.270 Fit side-chains outliers start: 24 outliers final: 18 residues processed: 229 average time/residue: 1.1199 time to fit residues: 274.7729 Evaluate side-chains 238 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 220 time to evaluate : 1.150 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 7 residues processed: 12 average time/residue: 0.4419 time to fit residues: 7.8041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 102 optimal weight: 0.0980 chunk 108 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 176 GLN B 220 GLN B 230 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.1447 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= 0.211 Angle : 0.521 14.458 12503 Z= 0.272 Chirality : 0.042 0.206 1421 Planarity : 0.003 0.030 1571 Dihedral : 4.125 22.101 1247 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.23 % Allowed : 14.80 % 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: 0.90 (0.25), residues: 1142 helix: 2.28 (0.27), residues: 397 sheet: 0.49 (0.29), residues: 301 loop : -0.89 (0.29), residues: 444 *********************** 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 257 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 215 time to evaluate : 1.031 Fit side-chains outliers start: 42 outliers final: 22 residues processed: 227 average time/residue: 1.1797 time to fit residues: 286.4170 Evaluate side-chains 227 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 205 time to evaluate : 0.915 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 8 residues processed: 15 average time/residue: 0.6685 time to fit residues: 12.3752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 0.0870 chunk 92 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 102 GLN 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9237 Z= 0.286 Angle : 0.564 14.981 12503 Z= 0.290 Chirality : 0.043 0.231 1421 Planarity : 0.004 0.032 1571 Dihedral : 4.204 22.469 1247 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.32 % Allowed : 16.92 % 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: 0.83 (0.25), residues: 1142 helix: 2.24 (0.27), residues: 397 sheet: 0.41 (0.29), residues: 301 loop : -0.91 (0.28), residues: 444 *********************** 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 257 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 224 time to evaluate : 1.131 Fit side-chains outliers start: 33 outliers final: 23 residues processed: 236 average time/residue: 1.1010 time to fit residues: 278.9681 Evaluate side-chains 249 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 226 time to evaluate : 0.995 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 8 residues processed: 15 average time/residue: 0.4214 time to fit residues: 8.7987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 104 optimal weight: 0.3980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 188 HIS ** 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: 0.7296 moved from start: 0.1634 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= 0.212 Angle : 0.538 14.878 12503 Z= 0.278 Chirality : 0.043 0.207 1421 Planarity : 0.003 0.033 1571 Dihedral : 4.105 21.782 1247 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.82 % Allowed : 17.93 % Favored : 79.25 % 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: 0.93 (0.25), residues: 1142 helix: 2.37 (0.27), residues: 396 sheet: 0.43 (0.29), residues: 300 loop : -0.88 (0.28), residues: 446 *********************** 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 246 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 218 time to evaluate : 1.012 Fit side-chains outliers start: 28 outliers final: 16 residues processed: 232 average time/residue: 1.1220 time to fit residues: 278.6036 Evaluate side-chains 231 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 215 time to evaluate : 0.926 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 9 residues processed: 7 average time/residue: 0.4509 time to fit residues: 5.1235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 188 HIS ** 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: 0.7303 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9237 Z= 0.243 Angle : 0.554 14.952 12503 Z= 0.284 Chirality : 0.043 0.218 1421 Planarity : 0.003 0.034 1571 Dihedral : 4.110 21.762 1247 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.12 % Allowed : 18.23 % 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: 0.91 (0.25), residues: 1142 helix: 2.35 (0.27), residues: 395 sheet: 0.43 (0.29), residues: 300 loop : -0.87 (0.28), residues: 447 *********************** 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 260 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 229 time to evaluate : 0.993 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 18 residues processed: 244 average time/residue: 1.0818 time to fit residues: 283.2719 Evaluate side-chains 246 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 228 time to evaluate : 0.950 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 8 residues processed: 10 average time/residue: 0.3739 time to fit residues: 5.8643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 0.0470 chunk 20 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 44 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: 0.7271 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9237 Z= 0.148 Angle : 0.521 14.167 12503 Z= 0.265 Chirality : 0.041 0.183 1421 Planarity : 0.003 0.032 1571 Dihedral : 3.935 19.925 1247 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.42 % Allowed : 19.44 % Favored : 78.15 % 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: 1.05 (0.25), residues: 1142 helix: 2.56 (0.27), residues: 396 sheet: 0.34 (0.29), residues: 301 loop : -0.78 (0.29), residues: 445 *********************** 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 239 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 215 time to evaluate : 1.022 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 15 residues processed: 226 average time/residue: 1.1540 time to fit residues: 279.4280 Evaluate side-chains 226 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 211 time to evaluate : 1.010 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 7 residues processed: 8 average time/residue: 0.7942 time to fit residues: 8.3880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 60 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 188 HIS ** 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: 0.7284 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9237 Z= 0.194 Angle : 0.554 14.081 12503 Z= 0.278 Chirality : 0.042 0.204 1421 Planarity : 0.003 0.033 1571 Dihedral : 3.973 19.883 1247 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.81 % Allowed : 20.44 % 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: 1.05 (0.25), residues: 1142 helix: 2.54 (0.27), residues: 397 sheet: 0.47 (0.29), residues: 297 loop : -0.86 (0.29), residues: 448 *********************** 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 230 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 212 time to evaluate : 0.927 Fit side-chains outliers start: 18 outliers final: 12 residues processed: 224 average time/residue: 1.1478 time to fit residues: 275.2256 Evaluate side-chains 226 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 214 time to evaluate : 0.963 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 4 average time/residue: 0.6111 time to fit residues: 4.1612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 102 optimal weight: 0.3980 chunk 88 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 188 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9237 Z= 0.169 Angle : 0.546 13.875 12503 Z= 0.276 Chirality : 0.042 0.194 1421 Planarity : 0.003 0.032 1571 Dihedral : 3.946 19.390 1247 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.81 % Allowed : 20.85 % Favored : 77.34 % 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: 1.12 (0.25), residues: 1142 helix: 2.61 (0.27), residues: 397 sheet: 0.52 (0.29), residues: 295 loop : -0.83 (0.29), residues: 450 ********************** 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 228 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 210 time to evaluate : 1.009 Fit side-chains outliers start: 18 outliers final: 12 residues processed: 221 average time/residue: 1.1821 time to fit residues: 279.2984 Evaluate side-chains 225 residues out of total 993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 213 time to evaluate : 0.993 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 7 residues processed: 5 average time/residue: 0.8145 time to fit residues: 5.8414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 88 optimal weight: 0.0980 chunk 37 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 188 HIS ** 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** S 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.142057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.121467 restraints weight = 11914.199| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.11 r_work: 0.3465 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9237 Z= 0.157 Angle : 0.548 13.530 12503 Z= 0.274 Chirality : 0.042 0.188 1421 Planarity : 0.003 0.032 1571 Dihedral : 3.909 18.839 1247 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.31 % Allowed : 21.75 % 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: 1.17 (0.26), residues: 1142 helix: 2.67 (0.27), residues: 397 sheet: 0.40 (0.30), residues: 298 loop : -0.70 (0.29), residues: 447 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4515.52 seconds wall clock time: 80 minutes 33.41 seconds (4833.41 seconds total)