Starting phenix.real_space_refine on Fri Nov 15 10:11:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yh5_39281/11_2024/8yh5_39281.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yh5_39281/11_2024/8yh5_39281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yh5_39281/11_2024/8yh5_39281.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yh5_39281/11_2024/8yh5_39281.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yh5_39281/11_2024/8yh5_39281.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yh5_39281/11_2024/8yh5_39281.cif" } resolution = 3.66 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= 1.084 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 66 5.16 5 C 5564 2.51 5 N 1462 2.21 5 O 1603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8695 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "A" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1700 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 208} Chain breaks: 2 Chain: "R" Number of atoms: 2198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2198 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain breaks: 1 Chain: "R" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'ZIR%rna3p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 5.30, per 1000 atoms: 0.61 Number of scatterers: 8695 At special positions: 0 Unit cell: (89.91, 122.1, 124.32, 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 66 16.00 O 1603 8.00 N 1462 7.00 C 5564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS B 114 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Simple disulfide: pdb=" SG CYS R 83 " - pdb=" SG CYS R 165 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.1 seconds 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2066 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 37.8% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.863A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 24 Processing helix chain 'G' and resid 33 through 44 removed outlier: 3.506A pdb=" N MET G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.706A 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 208 through 212 removed outlier: 3.576A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.501A pdb=" N LYS A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.541A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 275 through 281 removed outlier: 3.665A pdb=" N LYS A 279 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.682A pdb=" N ALA A 300 " --> pdb=" O TYR A 296 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.544A pdb=" N GLY A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 40 removed outlier: 3.659A pdb=" N LYS R 38 " --> pdb=" O ILE R 34 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN R 40 " --> pdb=" O VAL R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 64 removed outlier: 3.637A pdb=" N PHE R 50 " --> pdb=" O THR R 46 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 75 Processing helix chain 'R' and resid 79 through 115 removed outlier: 3.613A pdb=" N PHE R 93 " --> pdb=" O LEU R 89 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR R 94 " --> pdb=" O MET R 90 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR R 115 " --> pdb=" O ARG R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 122 Processing helix chain 'R' and resid 123 through 144 Processing helix chain 'R' and resid 145 through 148 removed outlier: 3.786A pdb=" N GLY R 148 " --> pdb=" O PRO R 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 145 through 148' Processing helix chain 'R' and resid 150 through 154 Processing helix chain 'R' and resid 166 through 171 removed outlier: 3.684A pdb=" N MET R 171 " --> pdb=" O PHE R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 179 removed outlier: 4.020A pdb=" N MET R 176 " --> pdb=" O ARG R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 185 Processing helix chain 'R' and resid 185 through 207 Processing helix chain 'R' and resid 225 through 254 removed outlier: 3.591A pdb=" N CYS R 241 " --> pdb=" O LEU R 237 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP R 242 " --> pdb=" O PHE R 238 " (cutoff:3.500A) Proline residue: R 244 - end of helix removed outlier: 3.561A pdb=" N TYR R 253 " --> pdb=" O ASN R 249 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE R 254 " --> pdb=" O CYS R 250 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 282 removed outlier: 3.517A pdb=" N ILE R 267 " --> pdb=" O LEU R 263 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER R 274 " --> pdb=" O SER R 270 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET R 275 " --> pdb=" O HIS R 271 " (cutoff:3.500A) Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 285 through 295 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.728A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.840A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.974A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA B 104 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA B 113 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 5.512A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER B 160 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.541A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.303A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.458A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.780A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.123A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY S 44 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 129 through 130 removed outlier: 3.591A pdb=" N PHE S 200 " --> pdb=" O CYS S 147 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 135 through 136 removed outlier: 6.049A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR S 216 " --> pdb=" O PHE S 165 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE S 165 " --> pdb=" O TYR S 216 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.500A pdb=" N PHE A 199 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) 392 hydrogen bonds defined for protein. 1107 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: 2.46 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2733 1.34 - 1.46: 1661 1.46 - 1.58: 4386 1.58 - 1.70: 0 1.70 - 1.82: 98 Bond restraints: 8878 Sorted by residual: bond pdb=" N ILE R 248 " pdb=" CA ILE R 248 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.19e-02 7.06e+03 9.16e+00 bond pdb=" N ARG S 18 " pdb=" CA ARG S 18 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.16e-02 7.43e+03 8.96e+00 bond pdb=" N LYS S 19 " pdb=" CA LYS S 19 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.25e-02 6.40e+03 8.42e+00 bond pdb=" N GLN B 259 " pdb=" CA GLN B 259 " ideal model delta sigma weight residual 1.454 1.489 -0.036 1.23e-02 6.61e+03 8.39e+00 bond pdb=" N ARG S 98 " pdb=" CA ARG S 98 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.15e-02 7.56e+03 7.68e+00 ... (remaining 8873 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 11314 1.37 - 2.73: 551 2.73 - 4.10: 130 4.10 - 5.47: 23 5.47 - 6.84: 5 Bond angle restraints: 12023 Sorted by residual: angle pdb=" N ASN R 249 " pdb=" CA ASN R 249 " pdb=" C ASN R 249 " ideal model delta sigma weight residual 113.28 107.60 5.68 1.22e+00 6.72e-01 2.17e+01 angle pdb=" CA ILE S 100 " pdb=" C ILE S 100 " pdb=" O ILE S 100 " ideal model delta sigma weight residual 120.36 115.52 4.84 1.06e+00 8.90e-01 2.08e+01 angle pdb=" N ILE R 185 " pdb=" CA ILE R 185 " pdb=" C ILE R 185 " ideal model delta sigma weight residual 112.12 108.39 3.73 8.40e-01 1.42e+00 1.97e+01 angle pdb=" N GLU G 22 " pdb=" CA GLU G 22 " pdb=" C GLU G 22 " ideal model delta sigma weight residual 112.54 107.53 5.01 1.22e+00 6.72e-01 1.69e+01 angle pdb=" CA ARG S 18 " pdb=" C ARG S 18 " pdb=" O ARG S 18 " ideal model delta sigma weight residual 121.89 116.71 5.18 1.27e+00 6.20e-01 1.67e+01 ... (remaining 12018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.20: 5044 25.20 - 50.40: 213 50.40 - 75.60: 17 75.60 - 100.80: 1 100.80 - 126.00: 1 Dihedral angle restraints: 5276 sinusoidal: 2074 harmonic: 3202 Sorted by residual: dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 136.18 -43.18 1 1.00e+01 1.00e-02 2.60e+01 dihedral pdb=" CD ARG S 18 " pdb=" NE ARG S 18 " pdb=" CZ ARG S 18 " pdb=" NH1 ARG S 18 " ideal model delta sinusoidal sigma weight residual 0.00 -41.92 41.92 1 1.00e+01 1.00e-02 2.46e+01 dihedral pdb=" CA PHE B 292 " pdb=" C PHE B 292 " pdb=" N ASN B 293 " pdb=" CA ASN B 293 " ideal model delta harmonic sigma weight residual -180.00 -155.35 -24.65 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 5273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1004 0.040 - 0.080: 258 0.080 - 0.121: 82 0.121 - 0.161: 24 0.161 - 0.201: 8 Chirality restraints: 1376 Sorted by residual: chirality pdb=" C3' ZIR R 801 " pdb=" C2' ZIR R 801 " pdb=" C4' ZIR R 801 " pdb=" O3' ZIR R 801 " both_signs ideal model delta sigma weight residual False -2.48 -2.68 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ILE R 248 " pdb=" N ILE R 248 " pdb=" C ILE R 248 " pdb=" CB ILE R 248 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.57e-01 chirality pdb=" CA ILE S 100 " pdb=" N ILE S 100 " pdb=" C ILE S 100 " pdb=" CB ILE S 100 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.13e-01 ... (remaining 1373 not shown) Planarity restraints: 1499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG S 18 " 0.713 9.50e-02 1.11e+02 3.20e-01 6.24e+01 pdb=" NE ARG S 18 " -0.044 2.00e-02 2.50e+03 pdb=" CZ ARG S 18 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG S 18 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG S 18 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 219 " -0.671 9.50e-02 1.11e+02 3.01e-01 5.51e+01 pdb=" NE ARG B 219 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG B 219 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG B 219 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 219 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 52 " -0.586 9.50e-02 1.11e+02 2.63e-01 4.23e+01 pdb=" NE ARG B 52 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG B 52 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG B 52 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 52 " -0.017 2.00e-02 2.50e+03 ... (remaining 1496 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 191 2.66 - 3.22: 8904 3.22 - 3.78: 13512 3.78 - 4.34: 18835 4.34 - 4.90: 30019 Nonbonded interactions: 71461 Sorted by model distance: nonbonded pdb=" OG1 THR B 184 " pdb=" OD2 ASP B 205 " model vdw 2.102 3.040 nonbonded pdb=" OG SER B 160 " pdb=" O VAL B 187 " model vdw 2.108 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.113 3.040 nonbonded pdb=" OE1 GLN R 260 " pdb=" OH TYR R 264 " model vdw 2.127 3.040 nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.150 3.040 ... (remaining 71456 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.030 Find NCS groups from input model: 0.090 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6122 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8878 Z= 0.270 Angle : 0.715 6.835 12023 Z= 0.452 Chirality : 0.045 0.201 1376 Planarity : 0.017 0.320 1499 Dihedral : 13.334 125.995 3198 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.10 % Allowed : 0.42 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.50 (0.26), residues: 1085 helix: 0.28 (0.27), residues: 375 sheet: -1.68 (0.30), residues: 290 loop : -1.51 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.006 0.001 HIS B 225 PHE 0.021 0.001 PHE A 267 TYR 0.012 0.001 TYR B 289 ARG 0.008 0.001 ARG R 172 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 GLU cc_start: 0.8491 (mp0) cc_final: 0.8262 (mp0) REVERT: B 260 GLU cc_start: 0.5471 (tt0) cc_final: 0.4674 (tm-30) REVERT: G 58 GLU cc_start: 0.8754 (mp0) cc_final: 0.8537 (mp0) REVERT: S 46 GLU cc_start: 0.6451 (tp30) cc_final: 0.6006 (tt0) REVERT: S 93 MET cc_start: 0.6921 (tpt) cc_final: 0.6669 (tpt) REVERT: S 190 ARG cc_start: 0.4456 (mtp-110) cc_final: 0.4223 (mtp180) REVERT: S 219 GLN cc_start: 0.3092 (pp30) cc_final: 0.2329 (pp30) REVERT: A 276 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7803 (mp0) REVERT: A 322 HIS cc_start: 0.6592 (t70) cc_final: 0.6254 (t-90) REVERT: A 333 GLN cc_start: 0.8519 (mm-40) cc_final: 0.8132 (mm-40) REVERT: A 345 LYS cc_start: 0.7926 (mptt) cc_final: 0.7539 (tptp) REVERT: R 173 MET cc_start: 0.8499 (mmt) cc_final: 0.8139 (mmt) outliers start: 1 outliers final: 0 residues processed: 229 average time/residue: 0.2392 time to fit residues: 73.2750 Evaluate side-chains 170 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 110 ASN B 230 ASN S 82 GLN S 219 GLN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS A 306 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 30 ASN ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8878 Z= 0.290 Angle : 0.730 10.190 12023 Z= 0.381 Chirality : 0.047 0.198 1376 Planarity : 0.004 0.036 1499 Dihedral : 6.398 118.415 1216 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.79 % Favored : 95.12 % Rotamer: Outliers : 2.94 % Allowed : 12.17 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.26), residues: 1085 helix: 0.42 (0.26), residues: 386 sheet: -1.32 (0.31), residues: 279 loop : -1.48 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 35 HIS 0.005 0.001 HIS A 188 PHE 0.022 0.002 PHE R 288 TYR 0.024 0.002 TYR S 178 ARG 0.005 0.001 ARG R 166 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 TRP cc_start: 0.7976 (m100) cc_final: 0.7768 (m100) REVERT: B 130 GLU cc_start: 0.8608 (mp0) cc_final: 0.8248 (mp0) REVERT: B 256 ARG cc_start: 0.7601 (mmp-170) cc_final: 0.7353 (mmp-170) REVERT: B 300 LEU cc_start: 0.9167 (mp) cc_final: 0.8917 (mp) REVERT: S 210 GLU cc_start: 0.7017 (mp0) cc_final: 0.6417 (mp0) REVERT: A 34 VAL cc_start: 0.7323 (OUTLIER) cc_final: 0.7028 (t) REVERT: A 216 GLU cc_start: 0.8221 (tt0) cc_final: 0.7812 (mt-10) REVERT: A 269 ASN cc_start: 0.6444 (OUTLIER) cc_final: 0.5925 (m-40) REVERT: A 289 GLU cc_start: 0.8840 (tp30) cc_final: 0.7975 (mp0) REVERT: A 313 ARG cc_start: 0.6528 (mtt180) cc_final: 0.5958 (mmt90) REVERT: A 345 LYS cc_start: 0.7705 (mptt) cc_final: 0.7348 (tptp) outliers start: 28 outliers final: 13 residues processed: 201 average time/residue: 0.2191 time to fit residues: 60.2738 Evaluate side-chains 174 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 189 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 HIS ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6443 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8878 Z= 0.241 Angle : 0.675 8.740 12023 Z= 0.349 Chirality : 0.045 0.211 1376 Planarity : 0.004 0.036 1499 Dihedral : 6.132 114.165 1216 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.57 % Allowed : 15.95 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.26), residues: 1085 helix: 0.65 (0.26), residues: 386 sheet: -1.33 (0.30), residues: 282 loop : -1.24 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 35 HIS 0.005 0.001 HIS A 244 PHE 0.017 0.002 PHE R 48 TYR 0.019 0.002 TYR S 178 ARG 0.009 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 TRP cc_start: 0.8039 (m100) cc_final: 0.7756 (m100) REVERT: B 130 GLU cc_start: 0.8734 (mp0) cc_final: 0.8313 (mp0) REVERT: G 22 GLU cc_start: 0.3428 (tp30) cc_final: 0.2777 (tp30) REVERT: S 126 ILE cc_start: 0.4647 (mm) cc_final: 0.4427 (tp) REVERT: S 148 ARG cc_start: 0.8418 (mmm-85) cc_final: 0.8149 (mmm-85) REVERT: S 190 ARG cc_start: 0.4984 (mtp180) cc_final: 0.4668 (mtp-110) REVERT: A 216 GLU cc_start: 0.8245 (tt0) cc_final: 0.7846 (mt-10) REVERT: A 289 GLU cc_start: 0.8902 (tp30) cc_final: 0.8109 (mp0) REVERT: A 313 ARG cc_start: 0.6402 (mtt180) cc_final: 0.6091 (mmt90) REVERT: R 117 ARG cc_start: 0.5394 (mtm-85) cc_final: 0.5107 (mtm-85) REVERT: R 140 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7757 (tp) REVERT: R 171 MET cc_start: 0.8602 (tpp) cc_final: 0.8254 (tpp) REVERT: R 268 LEU cc_start: 0.6506 (OUTLIER) cc_final: 0.6216 (tp) outliers start: 34 outliers final: 16 residues processed: 196 average time/residue: 0.2238 time to fit residues: 59.4714 Evaluate side-chains 179 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain R residue 268 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 10 optimal weight: 0.2980 chunk 47 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN S 171 GLN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8878 Z= 0.180 Angle : 0.632 8.837 12023 Z= 0.323 Chirality : 0.043 0.217 1376 Planarity : 0.004 0.036 1499 Dihedral : 5.822 113.007 1216 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.04 % Allowed : 17.84 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.64 (0.26), residues: 1085 helix: 0.87 (0.26), residues: 385 sheet: -1.11 (0.31), residues: 278 loop : -1.03 (0.33), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 184 HIS 0.004 0.001 HIS A 244 PHE 0.015 0.001 PHE S 200 TYR 0.020 0.001 TYR S 178 ARG 0.005 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 TRP cc_start: 0.7910 (m100) cc_final: 0.7631 (m100) REVERT: B 130 GLU cc_start: 0.8734 (mp0) cc_final: 0.8292 (mp0) REVERT: B 256 ARG cc_start: 0.7320 (mmp-170) cc_final: 0.6390 (mmp80) REVERT: G 21 MET cc_start: 0.7713 (ppp) cc_final: 0.7182 (ppp) REVERT: G 22 GLU cc_start: 0.3678 (tp30) cc_final: 0.2836 (tp30) REVERT: S 168 ARG cc_start: 0.8741 (tpt170) cc_final: 0.8333 (tpt170) REVERT: S 171 GLN cc_start: 0.8477 (mp10) cc_final: 0.7652 (mp10) REVERT: S 176 LEU cc_start: 0.7205 (mp) cc_final: 0.6933 (mp) REVERT: S 208 GLU cc_start: 0.8051 (mp0) cc_final: 0.7836 (pm20) REVERT: A 20 ASP cc_start: 0.6049 (m-30) cc_final: 0.5796 (m-30) REVERT: A 34 VAL cc_start: 0.7376 (OUTLIER) cc_final: 0.7070 (t) REVERT: A 186 GLU cc_start: 0.7440 (mp0) cc_final: 0.6982 (mp0) REVERT: A 216 GLU cc_start: 0.8186 (tt0) cc_final: 0.7784 (mt-10) REVERT: A 287 TYR cc_start: 0.7608 (m-80) cc_final: 0.7255 (m-80) REVERT: A 289 GLU cc_start: 0.9108 (tp30) cc_final: 0.8360 (mp0) REVERT: A 313 ARG cc_start: 0.6466 (mtt180) cc_final: 0.6124 (mmt90) REVERT: A 315 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7996 (p0) REVERT: R 117 ARG cc_start: 0.5219 (mtm-85) cc_final: 0.4862 (mtm-85) REVERT: R 140 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7591 (tp) outliers start: 29 outliers final: 19 residues processed: 197 average time/residue: 0.2282 time to fit residues: 60.4547 Evaluate side-chains 185 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 124 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain S residue 220 HIS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain R residue 268 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 53 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.5465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8878 Z= 0.258 Angle : 0.677 8.119 12023 Z= 0.350 Chirality : 0.044 0.223 1376 Planarity : 0.004 0.035 1499 Dihedral : 5.968 113.593 1216 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.71 % Favored : 94.19 % Rotamer: Outliers : 3.99 % Allowed : 19.52 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.26), residues: 1085 helix: 0.87 (0.26), residues: 388 sheet: -0.92 (0.32), residues: 266 loop : -1.10 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 184 HIS 0.004 0.001 HIS B 62 PHE 0.019 0.002 PHE R 181 TYR 0.017 0.002 TYR S 178 ARG 0.005 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 172 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 TRP cc_start: 0.8189 (m100) cc_final: 0.7952 (m100) REVERT: B 130 GLU cc_start: 0.8808 (mp0) cc_final: 0.8269 (mp0) REVERT: B 256 ARG cc_start: 0.7556 (mmp-170) cc_final: 0.7047 (mmp80) REVERT: G 21 MET cc_start: 0.7834 (ppp) cc_final: 0.7325 (ppp) REVERT: G 22 GLU cc_start: 0.4188 (tp30) cc_final: 0.3469 (tp30) REVERT: S 168 ARG cc_start: 0.8781 (tpt170) cc_final: 0.8432 (tpt170) REVERT: S 183 LEU cc_start: 0.8823 (mm) cc_final: 0.8592 (mm) REVERT: A 20 ASP cc_start: 0.6379 (OUTLIER) cc_final: 0.6160 (m-30) REVERT: A 249 LEU cc_start: 0.8002 (tp) cc_final: 0.7798 (tp) REVERT: A 275 GLU cc_start: 0.8156 (pp20) cc_final: 0.7681 (pm20) REVERT: A 289 GLU cc_start: 0.9085 (tp30) cc_final: 0.8345 (mp0) REVERT: A 313 ARG cc_start: 0.6450 (mtt180) cc_final: 0.6155 (mmt90) REVERT: A 315 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.8088 (p0) REVERT: R 117 ARG cc_start: 0.5521 (mtm-85) cc_final: 0.5064 (mtm-85) REVERT: R 140 LEU cc_start: 0.7994 (tt) cc_final: 0.7715 (tp) REVERT: R 171 MET cc_start: 0.8506 (tpp) cc_final: 0.8277 (tpp) outliers start: 38 outliers final: 24 residues processed: 198 average time/residue: 0.2230 time to fit residues: 59.9616 Evaluate side-chains 191 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 220 HIS Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 248 ILE Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain R residue 265 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.9990 chunk 20 optimal weight: 0.0370 chunk 61 optimal weight: 0.0770 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 0.0470 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 30.0000 chunk 55 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 overall best weight: 0.3714 ------------------------------------------------------------------------------- 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 306 GLN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6393 moved from start: 0.5757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8878 Z= 0.170 Angle : 0.668 12.235 12023 Z= 0.341 Chirality : 0.043 0.242 1376 Planarity : 0.003 0.032 1499 Dihedral : 5.821 111.890 1216 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.87 % Favored : 96.04 % Rotamer: Outliers : 3.04 % Allowed : 21.41 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.28 (0.26), residues: 1085 helix: 1.14 (0.26), residues: 384 sheet: -0.71 (0.32), residues: 265 loop : -0.95 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 184 HIS 0.004 0.001 HIS B 266 PHE 0.017 0.001 PHE S 200 TYR 0.019 0.001 TYR S 178 ARG 0.004 0.000 ARG S 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 TRP cc_start: 0.7996 (m100) cc_final: 0.7430 (m100) REVERT: B 130 GLU cc_start: 0.8775 (mp0) cc_final: 0.8215 (mp0) REVERT: B 234 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.6341 (m-80) REVERT: G 21 MET cc_start: 0.7925 (ppp) cc_final: 0.7465 (ppp) REVERT: G 22 GLU cc_start: 0.4027 (tp30) cc_final: 0.3371 (tp30) REVERT: S 168 ARG cc_start: 0.8643 (tpt170) cc_final: 0.8399 (tpt170) REVERT: S 176 LEU cc_start: 0.7608 (mp) cc_final: 0.7363 (mp) REVERT: S 206 ARG cc_start: 0.8892 (mpp80) cc_final: 0.8378 (mpp80) REVERT: A 20 ASP cc_start: 0.6154 (OUTLIER) cc_final: 0.5809 (m-30) REVERT: A 275 GLU cc_start: 0.8158 (pp20) cc_final: 0.7725 (pm20) REVERT: A 289 GLU cc_start: 0.9159 (tp30) cc_final: 0.8482 (mp0) REVERT: A 315 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.8107 (p0) REVERT: R 117 ARG cc_start: 0.5392 (mtm-85) cc_final: 0.4946 (mtm-85) REVERT: R 140 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7598 (tp) REVERT: R 171 MET cc_start: 0.8467 (tpp) cc_final: 0.8202 (tpp) REVERT: R 181 PHE cc_start: 0.5575 (t80) cc_final: 0.5268 (t80) outliers start: 29 outliers final: 17 residues processed: 195 average time/residue: 0.2334 time to fit residues: 61.0845 Evaluate side-chains 187 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 124 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 220 HIS Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 265 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.1980 chunk 60 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 58 optimal weight: 20.0000 chunk 105 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 220 HIS ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.6119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8878 Z= 0.294 Angle : 0.768 13.304 12023 Z= 0.388 Chirality : 0.047 0.256 1376 Planarity : 0.004 0.032 1499 Dihedral : 6.153 112.328 1216 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.08 % Favored : 93.82 % Rotamer: Outliers : 3.67 % Allowed : 22.67 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.26), residues: 1085 helix: 0.92 (0.26), residues: 388 sheet: -0.87 (0.32), residues: 260 loop : -0.95 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 184 HIS 0.004 0.001 HIS A 188 PHE 0.020 0.002 PHE R 181 TYR 0.017 0.002 TYR S 102 ARG 0.005 0.001 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 ASP cc_start: 0.7578 (t0) cc_final: 0.7199 (t0) REVERT: B 82 TRP cc_start: 0.8185 (m100) cc_final: 0.7713 (m100) REVERT: B 130 GLU cc_start: 0.8865 (mp0) cc_final: 0.8306 (mp0) REVERT: B 234 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.7025 (m-80) REVERT: G 21 MET cc_start: 0.8001 (ppp) cc_final: 0.7573 (ppp) REVERT: G 22 GLU cc_start: 0.4339 (tp30) cc_final: 0.3646 (tp30) REVERT: S 128 MET cc_start: 0.6275 (mmp) cc_final: 0.6017 (mmm) REVERT: S 168 ARG cc_start: 0.8760 (tpt170) cc_final: 0.8309 (tpt170) REVERT: S 206 ARG cc_start: 0.8968 (mpp80) cc_final: 0.8441 (mpp80) REVERT: A 20 ASP cc_start: 0.6264 (OUTLIER) cc_final: 0.6030 (m-30) REVERT: A 313 ARG cc_start: 0.6199 (mmt90) cc_final: 0.5969 (mmp80) REVERT: R 40 ASN cc_start: 0.7651 (t0) cc_final: 0.7203 (m-40) REVERT: R 117 ARG cc_start: 0.5490 (mtm-85) cc_final: 0.5099 (mtm-85) REVERT: R 140 LEU cc_start: 0.7986 (tt) cc_final: 0.7711 (tp) REVERT: R 152 LYS cc_start: 0.7985 (mmtp) cc_final: 0.7523 (mmtm) REVERT: R 171 MET cc_start: 0.8346 (tpp) cc_final: 0.8135 (tpp) outliers start: 35 outliers final: 21 residues processed: 185 average time/residue: 0.2147 time to fit residues: 54.4128 Evaluate side-chains 183 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 220 HIS Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain R residue 265 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 chunk 9 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 100 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.6334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8878 Z= 0.202 Angle : 0.736 11.831 12023 Z= 0.365 Chirality : 0.045 0.268 1376 Planarity : 0.004 0.032 1499 Dihedral : 6.041 111.732 1216 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.33 % Favored : 95.58 % Rotamer: Outliers : 3.36 % Allowed : 23.82 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.28 (0.26), residues: 1085 helix: 1.04 (0.26), residues: 385 sheet: -0.73 (0.32), residues: 263 loop : -0.84 (0.32), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 184 HIS 0.011 0.001 HIS S 220 PHE 0.019 0.001 PHE S 200 TYR 0.019 0.001 TYR S 178 ARG 0.010 0.000 ARG S 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 ASP cc_start: 0.7560 (t0) cc_final: 0.7197 (t0) REVERT: B 82 TRP cc_start: 0.8104 (m100) cc_final: 0.7611 (m100) REVERT: B 130 GLU cc_start: 0.8838 (mp0) cc_final: 0.8591 (mp0) REVERT: B 234 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.6914 (m-80) REVERT: B 266 HIS cc_start: 0.7003 (t-90) cc_final: 0.6741 (t-90) REVERT: G 21 MET cc_start: 0.7958 (ppp) cc_final: 0.7572 (ppp) REVERT: G 22 GLU cc_start: 0.4504 (tp30) cc_final: 0.3867 (tp30) REVERT: G 48 ASP cc_start: 0.6734 (OUTLIER) cc_final: 0.6383 (m-30) REVERT: S 128 MET cc_start: 0.6113 (mmp) cc_final: 0.5799 (mmm) REVERT: S 168 ARG cc_start: 0.8683 (tpt170) cc_final: 0.8252 (tpt170) REVERT: S 206 ARG cc_start: 0.9022 (mpp80) cc_final: 0.8671 (mpp80) REVERT: R 40 ASN cc_start: 0.7481 (t0) cc_final: 0.7188 (m-40) REVERT: R 140 LEU cc_start: 0.7950 (tt) cc_final: 0.7672 (tp) REVERT: R 152 LYS cc_start: 0.7931 (mmtp) cc_final: 0.7555 (mmtm) REVERT: R 171 MET cc_start: 0.8403 (tpp) cc_final: 0.8168 (tpp) outliers start: 32 outliers final: 23 residues processed: 190 average time/residue: 0.2237 time to fit residues: 57.6545 Evaluate side-chains 185 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 220 HIS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 99 MET Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 265 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 92 optimal weight: 0.0770 chunk 64 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 0.6569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8878 Z= 0.216 Angle : 0.758 12.292 12023 Z= 0.374 Chirality : 0.047 0.348 1376 Planarity : 0.004 0.049 1499 Dihedral : 6.050 109.750 1216 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.35 % Favored : 94.56 % Rotamer: Outliers : 3.04 % Allowed : 23.61 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.28 (0.26), residues: 1085 helix: 1.02 (0.26), residues: 385 sheet: -0.73 (0.32), residues: 263 loop : -0.81 (0.32), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.002 0.001 HIS S 155 PHE 0.017 0.001 PHE S 200 TYR 0.018 0.001 TYR S 102 ARG 0.008 0.000 ARG S 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 ASP cc_start: 0.7642 (t0) cc_final: 0.7248 (t0) REVERT: B 82 TRP cc_start: 0.8070 (m100) cc_final: 0.7651 (m100) REVERT: B 130 GLU cc_start: 0.8863 (mp0) cc_final: 0.8616 (mp0) REVERT: B 234 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.6994 (m-80) REVERT: G 21 MET cc_start: 0.7956 (ppp) cc_final: 0.7606 (ppp) REVERT: G 22 GLU cc_start: 0.4614 (tp30) cc_final: 0.3962 (tp30) REVERT: S 18 ARG cc_start: 0.6917 (tpt-90) cc_final: 0.6708 (tpt-90) REVERT: S 128 MET cc_start: 0.6106 (mmp) cc_final: 0.5807 (mmm) REVERT: S 168 ARG cc_start: 0.8720 (tpt170) cc_final: 0.8264 (tpt170) REVERT: A 244 HIS cc_start: 0.8845 (m170) cc_final: 0.8522 (m90) REVERT: R 40 ASN cc_start: 0.7224 (t0) cc_final: 0.7019 (m-40) REVERT: R 140 LEU cc_start: 0.8042 (tt) cc_final: 0.7776 (tp) REVERT: R 152 LYS cc_start: 0.8142 (mmtp) cc_final: 0.7787 (mmmt) REVERT: R 171 MET cc_start: 0.8414 (tpp) cc_final: 0.8162 (tpp) outliers start: 29 outliers final: 22 residues processed: 186 average time/residue: 0.2271 time to fit residues: 56.8561 Evaluate side-chains 182 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 220 HIS Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 99 MET Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 265 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 66 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 moved from start: 0.6730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8878 Z= 0.204 Angle : 0.775 12.365 12023 Z= 0.380 Chirality : 0.046 0.349 1376 Planarity : 0.004 0.034 1499 Dihedral : 6.035 110.074 1216 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.52 % Favored : 95.39 % Rotamer: Outliers : 2.73 % Allowed : 24.24 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.28 (0.26), residues: 1085 helix: 0.96 (0.26), residues: 386 sheet: -0.73 (0.32), residues: 265 loop : -0.74 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.003 0.001 HIS S 155 PHE 0.016 0.001 PHE S 200 TYR 0.018 0.001 TYR S 178 ARG 0.005 0.000 ARG S 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 ASP cc_start: 0.7634 (t0) cc_final: 0.7240 (t0) REVERT: B 82 TRP cc_start: 0.8065 (m100) cc_final: 0.7666 (m100) REVERT: B 130 GLU cc_start: 0.8851 (mp0) cc_final: 0.8461 (mp0) REVERT: B 234 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.6917 (m-80) REVERT: G 21 MET cc_start: 0.7986 (ppp) cc_final: 0.7655 (ppp) REVERT: G 22 GLU cc_start: 0.4569 (tp30) cc_final: 0.3897 (tp30) REVERT: S 18 ARG cc_start: 0.6863 (tpt-90) cc_final: 0.6540 (tpt-90) REVERT: S 128 MET cc_start: 0.6028 (mmp) cc_final: 0.5663 (mmm) REVERT: S 168 ARG cc_start: 0.8712 (tpt170) cc_final: 0.8416 (tpt170) REVERT: A 186 GLU cc_start: 0.7530 (mp0) cc_final: 0.7129 (mp0) REVERT: A 216 GLU cc_start: 0.8185 (tt0) cc_final: 0.7783 (mt-10) REVERT: A 336 PHE cc_start: 0.8864 (t80) cc_final: 0.8565 (t80) REVERT: R 140 LEU cc_start: 0.8064 (tt) cc_final: 0.7792 (tp) REVERT: R 152 LYS cc_start: 0.8180 (mmtp) cc_final: 0.7810 (mmmt) outliers start: 26 outliers final: 24 residues processed: 191 average time/residue: 0.2307 time to fit residues: 59.3492 Evaluate side-chains 193 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 220 HIS Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 99 MET Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 265 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 10 optimal weight: 0.0570 chunk 15 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.161135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.133010 restraints weight = 19520.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.136573 restraints weight = 11482.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.138986 restraints weight = 8142.673| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.6876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8878 Z= 0.212 Angle : 0.787 12.558 12023 Z= 0.387 Chirality : 0.046 0.340 1376 Planarity : 0.004 0.042 1499 Dihedral : 6.128 109.242 1216 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.79 % Favored : 95.12 % Rotamer: Outliers : 2.94 % Allowed : 24.55 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.26 (0.26), residues: 1085 helix: 0.97 (0.26), residues: 386 sheet: -0.67 (0.32), residues: 263 loop : -0.76 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 82 HIS 0.002 0.001 HIS S 155 PHE 0.015 0.001 PHE S 200 TYR 0.018 0.001 TYR S 178 ARG 0.008 0.001 ARG A 313 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2057.90 seconds wall clock time: 38 minutes 34.41 seconds (2314.41 seconds total)