Starting phenix.real_space_refine on Thu Mar 14 22:38:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7s_28909/03_2024/8f7s_28909_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7s_28909/03_2024/8f7s_28909.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7s_28909/03_2024/8f7s_28909.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7s_28909/03_2024/8f7s_28909.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7s_28909/03_2024/8f7s_28909_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7s_28909/03_2024/8f7s_28909_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 84 5.16 5 C 6523 2.51 5 N 1617 2.21 5 O 1751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 76": "NH1" <-> "NH2" Residue "R ARG 146": "NH1" <-> "NH2" Residue "R ARG 160": "NH1" <-> "NH2" Residue "R ARG 190": "NH1" <-> "NH2" Residue "R ARG 239": "NH1" <-> "NH2" Residue "R ARG 244": "NH1" <-> "NH2" Residue "R ARG 254": "NH1" <-> "NH2" Residue "R ARG 258": "NH1" <-> "NH2" Residue "R ARG 291": "NH1" <-> "NH2" Residue "R ARG 292": "NH1" <-> "NH2" Residue "R ARG 327": "NH1" <-> "NH2" Residue "R ARG 330": "NH1" <-> "NH2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 27": "NH1" <-> "NH2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D ARG 160": "NH1" <-> "NH2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D ARG 239": "NH1" <-> "NH2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D ARG 258": "NH1" <-> "NH2" Residue "D ARG 291": "NH1" <-> "NH2" Residue "D ARG 292": "NH1" <-> "NH2" Residue "D ARG 327": "NH1" <-> "NH2" Residue "D ARG 330": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9975 Number of models: 1 Model: "" Number of chains: 10 Chain: "R" Number of atoms: 2268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2268 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 276} Chain: "P" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 56 Unusual residues: {'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 1} Modifications used: {'PEPT-D': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 6} Chain: "A" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1783 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 218} Chain breaks: 2 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "D" Number of atoms: 2268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2268 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 276} Chain: "Q" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 56 Unusual residues: {'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 1} Modifications used: {'PEPT-D': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 6} Chain: "F" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Modifications used: {'COO': 1} Link IDs: {'TRANS': 18} Chain: "R" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 182 Unusual residues: {'CLR': 2, 'PLM': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 174 Unusual residues: {'CLR': 3, 'PLM': 5} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 6.67, per 1000 atoms: 0.67 Number of scatterers: 9975 At special positions: 0 Unit cell: (143.64, 118.44, 105, 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 84 16.00 O 1751 8.00 N 1617 7.00 C 6523 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 121 " - pdb=" SG CYS R 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 121 " - pdb=" SG CYS D 198 " distance=2.03 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: 3.92 Conformation dependent library (CDL) restraints added in 1.7 seconds 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL P 2 " pdb=" CB DAL Q 2 " Number of C-beta restraints generated: 2332 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 10 sheets defined 54.4% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'R' and resid 46 through 76 Processing helix chain 'R' and resid 83 through 111 removed outlier: 4.094A pdb=" N THR R 101 " --> pdb=" O LEU R 97 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU R 102 " --> pdb=" O ALA R 98 " (cutoff:3.500A) Proline residue: R 103 - end of helix Processing helix chain 'R' and resid 118 through 151 Processing helix chain 'R' and resid 153 through 159 removed outlier: 3.564A pdb=" N LEU R 157 " --> pdb=" O PRO R 153 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP R 158 " --> pdb=" O VAL R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 162 through 186 removed outlier: 3.750A pdb=" N SER R 177 " --> pdb=" O TRP R 173 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY R 178 " --> pdb=" O VAL R 174 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL R 179 " --> pdb=" O LEU R 175 " (cutoff:3.500A) Proline residue: R 182 - end of helix Processing helix chain 'R' and resid 206 through 242 removed outlier: 4.943A pdb=" N VAL R 224 " --> pdb=" O PHE R 220 " (cutoff:3.500A) Proline residue: R 225 - end of helix removed outlier: 3.715A pdb=" N ARG R 241 " --> pdb=" O LEU R 237 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N SER R 242 " --> pdb=" O LEU R 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 244 through 246 No H-bonds generated for 'chain 'R' and resid 244 through 246' Processing helix chain 'R' and resid 250 through 286 removed outlier: 4.212A pdb=" N VAL R 266 " --> pdb=" O MET R 262 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL R 267 " --> pdb=" O VAL R 263 " (cutoff:3.500A) Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 294 through 321 removed outlier: 3.789A pdb=" N ASN R 314 " --> pdb=" O ASN R 310 " (cutoff:3.500A) Proline residue: R 315 - end of helix Processing helix chain 'R' and resid 323 through 332 Processing helix chain 'A' and resid 7 through 32 removed outlier: 4.018A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 208 through 216 removed outlier: 4.894A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 230 removed outlier: 4.274A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.525A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.555A pdb=" N CYS A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'B' and resid 9 through 30 Processing helix chain 'B' and resid 35 through 41 removed outlier: 5.401A pdb=" N ASN B 41 " --> pdb=" O GLN B 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 23 removed outlier: 3.528A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU C 22 " --> pdb=" O GLN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'D' and resid 46 through 76 Processing helix chain 'D' and resid 83 through 111 removed outlier: 4.097A pdb=" N THR D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU D 102 " --> pdb=" O ALA D 98 " (cutoff:3.500A) Proline residue: D 103 - end of helix Processing helix chain 'D' and resid 118 through 151 Processing helix chain 'D' and resid 153 through 159 removed outlier: 3.539A pdb=" N LEU D 157 " --> pdb=" O PRO D 153 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 186 removed outlier: 3.540A pdb=" N GLY D 178 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL D 179 " --> pdb=" O LEU D 175 " (cutoff:3.500A) Proline residue: D 182 - end of helix Processing helix chain 'D' and resid 206 through 242 removed outlier: 4.893A pdb=" N VAL D 224 " --> pdb=" O PHE D 220 " (cutoff:3.500A) Proline residue: D 225 - end of helix removed outlier: 3.716A pdb=" N ARG D 241 " --> pdb=" O LEU D 237 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N SER D 242 " --> pdb=" O LEU D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 286 removed outlier: 4.257A pdb=" N VAL D 266 " --> pdb=" O MET D 262 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL D 267 " --> pdb=" O VAL D 263 " (cutoff:3.500A) Proline residue: D 276 - end of helix Processing helix chain 'D' and resid 294 through 321 removed outlier: 4.077A pdb=" N ASN D 314 " --> pdb=" O ASN D 310 " (cutoff:3.500A) Proline residue: D 315 - end of helix Processing helix chain 'D' and resid 323 through 332 removed outlier: 3.617A pdb=" N PHE D 329 " --> pdb=" O PHE D 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 351 Processing sheet with id= A, first strand: chain 'R' and resid 187 through 192 removed outlier: 3.575A pdb=" N MET R 199 " --> pdb=" O VAL R 188 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG R 190 " --> pdb=" O VAL R 197 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.944A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 63 through 68 removed outlier: 6.852A pdb=" N ALA B 78 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N MET B 66 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL B 76 " --> pdb=" O MET B 66 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N TRP B 68 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU B 74 " --> pdb=" O TRP B 68 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASP B 88 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LYS B 94 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 107 through 110 removed outlier: 6.225A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 151 through 156 removed outlier: 6.823A pdb=" N SER B 165 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N CYS B 154 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL B 163 " --> pdb=" O CYS B 154 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N PHE B 156 " --> pdb=" O GLN B 161 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N GLN B 161 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR B 183 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 192 through 197 removed outlier: 7.096A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.762A pdb=" N GLY B 249 " --> pdb=" O ASN B 235 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE B 237 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA B 247 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N PHE B 239 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ALA B 245 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 278 through 283 removed outlier: 6.591A pdb=" N GLY B 293 " --> pdb=" O THR B 279 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL B 281 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU B 291 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N PHE B 283 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU B 289 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 341 through 344 Processing sheet with id= J, first strand: chain 'D' and resid 187 through 192 removed outlier: 3.534A pdb=" N MET D 199 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG D 190 " --> pdb=" O VAL D 197 " (cutoff:3.500A) 558 hydrogen bonds defined for protein. 1638 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: 2.54 Time building geometry restraints manager: 4.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3060 1.35 - 1.46: 2175 1.46 - 1.58: 4813 1.58 - 1.70: 0 1.70 - 1.82: 121 Bond restraints: 10169 Sorted by residual: bond pdb=" C GLY Q 7 " pdb=" N NH2 Q 8 " ideal model delta sigma weight residual 1.329 1.471 -0.142 1.40e-02 5.10e+03 1.03e+02 bond pdb=" C GLY P 7 " pdb=" N NH2 P 8 " ideal model delta sigma weight residual 1.329 1.470 -0.141 1.40e-02 5.10e+03 1.02e+02 bond pdb=" CA ALA R 275 " pdb=" C ALA R 275 " ideal model delta sigma weight residual 1.521 1.544 -0.023 1.14e-02 7.69e+03 4.01e+00 bond pdb=" C ALA D 275 " pdb=" N PRO D 276 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.20e-02 6.94e+03 3.82e+00 bond pdb=" C VAL R 224 " pdb=" N PRO R 225 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.36e-02 5.41e+03 3.59e+00 ... (remaining 10164 not shown) Histogram of bond angle deviations from ideal: 99.77 - 106.64: 250 106.64 - 113.52: 5841 113.52 - 120.40: 3770 120.40 - 127.28: 3788 127.28 - 134.16: 102 Bond angle restraints: 13751 Sorted by residual: angle pdb=" N LEU R 102 " pdb=" CA LEU R 102 " pdb=" C LEU R 102 " ideal model delta sigma weight residual 113.16 118.79 -5.63 1.42e+00 4.96e-01 1.57e+01 angle pdb=" N LEU D 102 " pdb=" CA LEU D 102 " pdb=" C LEU D 102 " ideal model delta sigma weight residual 113.16 118.74 -5.58 1.42e+00 4.96e-01 1.54e+01 angle pdb=" C ILE B 86 " pdb=" N TRP B 87 " pdb=" CA TRP B 87 " ideal model delta sigma weight residual 121.32 129.21 -7.89 2.10e+00 2.27e-01 1.41e+01 angle pdb=" N GLU R 112 " pdb=" CA GLU R 112 " pdb=" C GLU R 112 " ideal model delta sigma weight residual 113.56 108.52 5.04 1.39e+00 5.18e-01 1.32e+01 angle pdb=" N GLU D 112 " pdb=" CA GLU D 112 " pdb=" C GLU D 112 " ideal model delta sigma weight residual 113.56 108.58 4.98 1.39e+00 5.18e-01 1.29e+01 ... (remaining 13746 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.84: 5888 11.84 - 23.68: 368 23.68 - 35.52: 68 35.52 - 47.36: 16 47.36 - 59.20: 8 Dihedral angle restraints: 6348 sinusoidal: 2760 harmonic: 3588 Sorted by residual: dihedral pdb=" CA THR B 254 " pdb=" C THR B 254 " pdb=" N CYS B 255 " pdb=" CA CYS B 255 " ideal model delta harmonic sigma weight residual 180.00 162.89 17.11 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA PHE B 156 " pdb=" C PHE B 156 " pdb=" N LEU B 157 " pdb=" CA LEU B 157 " ideal model delta harmonic sigma weight residual 180.00 164.95 15.05 0 5.00e+00 4.00e-02 9.06e+00 dihedral pdb=" CA TRP B 302 " pdb=" C TRP B 302 " pdb=" N ASP B 303 " pdb=" CA ASP B 303 " ideal model delta harmonic sigma weight residual 180.00 165.13 14.87 0 5.00e+00 4.00e-02 8.85e+00 ... (remaining 6345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1444 0.082 - 0.164: 142 0.164 - 0.246: 17 0.246 - 0.328: 7 0.328 - 0.410: 5 Chirality restraints: 1615 Sorted by residual: chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" C14 CLR D 403 " pdb=" C13 CLR D 403 " pdb=" C15 CLR D 403 " pdb=" C8 CLR D 403 " both_signs ideal model delta sigma weight residual False -2.32 -2.72 0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" C14 CLR D 404 " pdb=" C13 CLR D 404 " pdb=" C15 CLR D 404 " pdb=" C8 CLR D 404 " both_signs ideal model delta sigma weight residual False -2.32 -2.71 0.40 2.00e-01 2.50e+01 3.94e+00 ... (remaining 1612 not shown) Planarity restraints: 1660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 240 " 0.043 5.00e-02 4.00e+02 6.45e-02 6.66e+00 pdb=" N PRO B 241 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 241 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 241 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG R 190 " -0.037 5.00e-02 4.00e+02 5.63e-02 5.08e+00 pdb=" N PRO R 191 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO R 191 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO R 191 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 190 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO D 191 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO D 191 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 191 " 0.031 5.00e-02 4.00e+02 ... (remaining 1657 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2327 2.81 - 3.33: 9096 3.33 - 3.86: 15704 3.86 - 4.38: 17899 4.38 - 4.90: 32040 Nonbonded interactions: 77066 Sorted by model distance: nonbonded pdb=" OG1 THR R 99 " pdb=" OG SER R 312 " model vdw 2.290 2.440 nonbonded pdb=" OH TYR R 208 " pdb=" O LEU D 237 " model vdw 2.292 2.440 nonbonded pdb=" O LEU R 237 " pdb=" OH TYR D 208 " model vdw 2.305 2.440 nonbonded pdb=" OE2 GLU B 265 " pdb=" OG1 THR B 268 " model vdw 2.312 2.440 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.342 2.520 ... (remaining 77061 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'D' and (resid 45 through 333 or resid 406 through 408)) selection = (chain 'R' and (resid 45 through 333 or resid 406 through 408)) } ncs_group { reference = chain 'P' selection = chain 'Q' } 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: 0.670 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: 4.230 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 29.930 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 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 0.142 10169 Z= 0.292 Angle : 0.870 8.024 13751 Z= 0.474 Chirality : 0.059 0.410 1615 Planarity : 0.006 0.065 1660 Dihedral : 8.472 59.200 4010 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.29 (0.22), residues: 1203 helix: 1.68 (0.16), residues: 677 sheet: 1.03 (0.42), residues: 158 loop : -0.75 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 209 HIS 0.006 0.001 HIS C 44 PHE 0.029 0.002 PHE R 325 TYR 0.027 0.002 TYR D 87 ARG 0.008 0.001 ARG R 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 1.041 Fit side-chains REVERT: R 190 ARG cc_start: 0.5956 (mtt180) cc_final: 0.5732 (mtt180) REVERT: R 220 PHE cc_start: 0.8204 (m-80) cc_final: 0.8000 (m-80) REVERT: A 22 ASN cc_start: 0.7411 (m-40) cc_final: 0.7192 (m-40) REVERT: A 216 GLU cc_start: 0.7625 (tt0) cc_final: 0.7406 (tt0) REVERT: A 251 ASP cc_start: 0.7559 (t0) cc_final: 0.7312 (t70) REVERT: B 70 THR cc_start: 0.8076 (m) cc_final: 0.7732 (p) REVERT: B 175 ASP cc_start: 0.7289 (t0) cc_final: 0.7086 (t70) REVERT: B 217 ASP cc_start: 0.7542 (t0) cc_final: 0.7150 (t0) REVERT: D 184 MET cc_start: 0.7860 (ttm) cc_final: 0.7643 (ttp) outliers start: 0 outliers final: 1 residues processed: 258 average time/residue: 1.1713 time to fit residues: 323.4851 Evaluate side-chains 165 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 170 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.5980 chunk 88 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 35 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 105 GLN R 169 ASN R 201 GLN ** R 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 269 ASN A 306 GLN B 93 ASN B 181 GLN C 44 HIS D 67 ASN D 85 ASN D 169 ASN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10169 Z= 0.174 Angle : 0.512 7.813 13751 Z= 0.271 Chirality : 0.039 0.143 1615 Planarity : 0.005 0.051 1660 Dihedral : 7.095 57.433 1819 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.84 % Allowed : 10.04 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.23), residues: 1203 helix: 2.71 (0.18), residues: 665 sheet: 1.24 (0.41), residues: 167 loop : -0.62 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 87 HIS 0.004 0.001 HIS B 147 PHE 0.013 0.001 PHE A 189 TYR 0.019 0.002 TYR A 296 ARG 0.006 0.001 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 156 time to evaluate : 0.986 Fit side-chains REVERT: A 22 ASN cc_start: 0.7616 (m-40) cc_final: 0.7217 (m-40) REVERT: A 26 ASP cc_start: 0.6736 (m-30) cc_final: 0.6501 (m-30) REVERT: A 53 MET cc_start: 0.6683 (OUTLIER) cc_final: 0.5715 (mpt) REVERT: A 275 GLU cc_start: 0.7451 (tp30) cc_final: 0.6819 (tp30) REVERT: B 47 ARG cc_start: 0.6378 (mmm-85) cc_final: 0.6024 (mmt90) REVERT: B 70 THR cc_start: 0.8121 (m) cc_final: 0.7871 (p) REVERT: B 151 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8233 (mp) REVERT: B 217 ASP cc_start: 0.7650 (t0) cc_final: 0.7276 (t0) REVERT: D 158 ASP cc_start: 0.5896 (m-30) cc_final: 0.5667 (m-30) outliers start: 30 outliers final: 10 residues processed: 173 average time/residue: 1.1846 time to fit residues: 219.9092 Evaluate side-chains 152 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 85 ASN Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 178 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 169 ASN R 314 ASN A 213 HIS A 306 GLN B 37 GLN B 273 ASN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN D 105 GLN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10169 Z= 0.345 Angle : 0.635 9.131 13751 Z= 0.333 Chirality : 0.044 0.147 1615 Planarity : 0.005 0.051 1660 Dihedral : 8.520 59.821 1817 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.98 % Allowed : 10.04 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.86 (0.23), residues: 1203 helix: 2.26 (0.18), residues: 665 sheet: 1.45 (0.42), residues: 156 loop : -0.75 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 87 HIS 0.007 0.002 HIS B 147 PHE 0.017 0.002 PHE A 354 TYR 0.019 0.002 TYR P 1 ARG 0.008 0.001 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 139 time to evaluate : 1.224 Fit side-chains REVERT: R 111 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.6500 (mpt) REVERT: R 302 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8126 (mp) REVERT: A 17 LYS cc_start: 0.7106 (OUTLIER) cc_final: 0.6902 (mmtp) REVERT: A 22 ASN cc_start: 0.7577 (m-40) cc_final: 0.7232 (m-40) REVERT: B 175 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.7308 (t0) REVERT: B 217 ASP cc_start: 0.7724 (t0) cc_final: 0.7285 (t0) REVERT: C 21 MET cc_start: 0.5688 (mmm) cc_final: 0.5269 (ptm) REVERT: D 158 ASP cc_start: 0.6050 (m-30) cc_final: 0.5816 (m-30) REVERT: D 193 ASP cc_start: 0.6322 (t0) cc_final: 0.5945 (m-30) outliers start: 42 outliers final: 22 residues processed: 162 average time/residue: 1.2767 time to fit residues: 221.6642 Evaluate side-chains 149 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 123 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 LYS Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 111 MET Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 206 SER Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain D residue 263 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 50 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10169 Z= 0.137 Angle : 0.458 8.158 13751 Z= 0.244 Chirality : 0.037 0.147 1615 Planarity : 0.004 0.049 1660 Dihedral : 7.487 59.279 1817 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.94 % Allowed : 13.07 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.23), residues: 1203 helix: 2.74 (0.19), residues: 664 sheet: 1.37 (0.42), residues: 155 loop : -0.74 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 87 HIS 0.003 0.001 HIS B 147 PHE 0.016 0.001 PHE A 354 TYR 0.008 0.001 TYR R 87 ARG 0.005 0.000 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 134 time to evaluate : 1.175 Fit side-chains REVERT: R 189 THR cc_start: 0.8170 (m) cc_final: 0.7965 (t) REVERT: R 302 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8103 (mp) REVERT: A 22 ASN cc_start: 0.7486 (m-40) cc_final: 0.7252 (m-40) REVERT: B 47 ARG cc_start: 0.6415 (mmm-85) cc_final: 0.6099 (mmt90) REVERT: B 217 ASP cc_start: 0.7663 (t0) cc_final: 0.7243 (t0) REVERT: C 21 MET cc_start: 0.5815 (mmm) cc_final: 0.5274 (ptm) REVERT: D 155 LYS cc_start: 0.6681 (mttm) cc_final: 0.6464 (mttp) REVERT: D 158 ASP cc_start: 0.5997 (m-30) cc_final: 0.5762 (m-30) outliers start: 31 outliers final: 15 residues processed: 150 average time/residue: 1.2117 time to fit residues: 195.0469 Evaluate side-chains 148 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 199 MET Chi-restraints excluded: chain R residue 265 VAL Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain D residue 263 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 10169 Z= 0.355 Angle : 0.654 9.908 13751 Z= 0.340 Chirality : 0.044 0.160 1615 Planarity : 0.005 0.051 1660 Dihedral : 8.951 57.494 1817 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.17 % Allowed : 12.31 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.65 (0.23), residues: 1203 helix: 2.14 (0.19), residues: 663 sheet: 1.32 (0.41), residues: 156 loop : -0.90 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 87 HIS 0.007 0.001 HIS B 147 PHE 0.018 0.003 PHE A 307 TYR 0.022 0.002 TYR P 1 ARG 0.007 0.001 ARG R 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 128 time to evaluate : 1.147 Fit side-chains REVERT: R 45 SER cc_start: 0.6201 (p) cc_final: 0.5722 (t) REVERT: R 111 MET cc_start: 0.8353 (mtm) cc_final: 0.8071 (mpp) REVERT: R 302 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8140 (mp) REVERT: A 17 LYS cc_start: 0.7088 (OUTLIER) cc_final: 0.6886 (mmtp) REVERT: B 134 ARG cc_start: 0.5908 (ptp-170) cc_final: 0.5687 (tpt170) REVERT: B 175 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7373 (t0) REVERT: B 217 ASP cc_start: 0.7676 (t0) cc_final: 0.7296 (t0) REVERT: B 222 MET cc_start: 0.6620 (OUTLIER) cc_final: 0.5908 (ppp) REVERT: C 21 MET cc_start: 0.5920 (mmm) cc_final: 0.5226 (ptm) REVERT: D 155 LYS cc_start: 0.6906 (mttm) cc_final: 0.6634 (mttp) REVERT: D 158 ASP cc_start: 0.6115 (m-30) cc_final: 0.5903 (m-30) REVERT: D 199 MET cc_start: 0.7089 (ptp) cc_final: 0.6717 (ptt) outliers start: 44 outliers final: 22 residues processed: 156 average time/residue: 1.1976 time to fit residues: 200.5940 Evaluate side-chains 149 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 123 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 206 SER Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 265 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 0.0170 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 201 GLN A 306 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10169 Z= 0.157 Angle : 0.486 8.767 13751 Z= 0.256 Chirality : 0.038 0.145 1615 Planarity : 0.004 0.047 1660 Dihedral : 7.911 59.185 1817 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.56 % Allowed : 14.30 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.24), residues: 1203 helix: 2.56 (0.19), residues: 665 sheet: 1.31 (0.40), residues: 158 loop : -0.79 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 87 HIS 0.003 0.001 HIS B 147 PHE 0.011 0.001 PHE A 354 TYR 0.011 0.001 TYR P 1 ARG 0.007 0.001 ARG R 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 129 time to evaluate : 1.210 Fit side-chains REVERT: R 45 SER cc_start: 0.6123 (p) cc_final: 0.5688 (t) REVERT: R 111 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7833 (mpp) REVERT: R 201 GLN cc_start: 0.7272 (tt0) cc_final: 0.7047 (tt0) REVERT: A 269 ASN cc_start: 0.7403 (m-40) cc_final: 0.7117 (m110) REVERT: B 134 ARG cc_start: 0.5981 (ptp-170) cc_final: 0.5715 (tpt170) REVERT: B 217 ASP cc_start: 0.7658 (t0) cc_final: 0.7281 (t0) REVERT: C 21 MET cc_start: 0.5983 (mmm) cc_final: 0.5283 (ptm) REVERT: D 155 LYS cc_start: 0.6803 (mttm) cc_final: 0.6561 (mttp) REVERT: D 158 ASP cc_start: 0.5967 (m-30) cc_final: 0.5742 (m-30) REVERT: D 199 MET cc_start: 0.6948 (ptp) cc_final: 0.6541 (ptt) outliers start: 27 outliers final: 13 residues processed: 143 average time/residue: 1.2987 time to fit residues: 198.7407 Evaluate side-chains 143 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 111 MET Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 206 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain D residue 263 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.8980 chunk 64 optimal weight: 0.1980 chunk 82 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10169 Z= 0.228 Angle : 0.545 9.647 13751 Z= 0.284 Chirality : 0.040 0.145 1615 Planarity : 0.004 0.048 1660 Dihedral : 8.224 59.528 1817 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.12 % Allowed : 13.73 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.98 (0.24), residues: 1203 helix: 2.45 (0.19), residues: 665 sheet: 1.24 (0.40), residues: 158 loop : -0.79 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 87 HIS 0.005 0.001 HIS B 147 PHE 0.013 0.002 PHE A 307 TYR 0.018 0.002 TYR P 1 ARG 0.006 0.001 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 127 time to evaluate : 1.152 Fit side-chains REVERT: R 45 SER cc_start: 0.6124 (p) cc_final: 0.5836 (t) REVERT: R 111 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7831 (mpp) REVERT: R 186 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.7096 (ttp) REVERT: R 323 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6164 (mp0) REVERT: A 269 ASN cc_start: 0.7413 (m-40) cc_final: 0.7150 (m110) REVERT: B 134 ARG cc_start: 0.6081 (ptp-170) cc_final: 0.5842 (tpt170) REVERT: B 217 ASP cc_start: 0.7644 (t0) cc_final: 0.7252 (t0) REVERT: B 222 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.6814 (pmm) REVERT: B 224 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7252 (mpt180) REVERT: C 21 MET cc_start: 0.5863 (mmm) cc_final: 0.5183 (ptm) REVERT: D 155 LYS cc_start: 0.6852 (mttm) cc_final: 0.6576 (mttp) REVERT: D 158 ASP cc_start: 0.5980 (m-30) cc_final: 0.5757 (m-30) REVERT: D 199 MET cc_start: 0.6969 (ptp) cc_final: 0.6558 (ptt) outliers start: 33 outliers final: 19 residues processed: 145 average time/residue: 1.2554 time to fit residues: 195.1889 Evaluate side-chains 148 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 124 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 85 ASN Chi-restraints excluded: chain R residue 111 MET Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 186 MET Chi-restraints excluded: chain R residue 206 SER Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain R residue 323 GLU Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain D residue 263 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 201 GLN A 306 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10169 Z= 0.192 Angle : 0.513 9.392 13751 Z= 0.267 Chirality : 0.039 0.146 1615 Planarity : 0.004 0.048 1660 Dihedral : 8.082 58.715 1817 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.12 % Allowed : 14.11 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.24), residues: 1203 helix: 2.51 (0.19), residues: 666 sheet: 1.15 (0.40), residues: 159 loop : -0.80 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 87 HIS 0.004 0.001 HIS B 147 PHE 0.012 0.002 PHE B 227 TYR 0.016 0.001 TYR P 1 ARG 0.006 0.001 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 126 time to evaluate : 1.150 Fit side-chains REVERT: R 45 SER cc_start: 0.6125 (p) cc_final: 0.5850 (t) REVERT: R 111 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7865 (mpp) REVERT: R 186 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.7101 (ttp) REVERT: R 192 ARG cc_start: 0.6827 (ttm170) cc_final: 0.6541 (ttp80) REVERT: A 17 LYS cc_start: 0.6906 (mttm) cc_final: 0.6547 (mttp) REVERT: A 269 ASN cc_start: 0.7443 (m-40) cc_final: 0.7185 (m110) REVERT: B 134 ARG cc_start: 0.6176 (ptp-170) cc_final: 0.5892 (tpt170) REVERT: B 217 ASP cc_start: 0.7646 (t0) cc_final: 0.7233 (t0) REVERT: B 222 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6810 (pmm) REVERT: B 224 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.7136 (mpt180) REVERT: C 21 MET cc_start: 0.5852 (mmm) cc_final: 0.5175 (ptm) REVERT: D 155 LYS cc_start: 0.6833 (mttm) cc_final: 0.6571 (mttp) REVERT: D 158 ASP cc_start: 0.5971 (m-30) cc_final: 0.5748 (m-30) REVERT: D 199 MET cc_start: 0.6950 (ptp) cc_final: 0.6528 (ptt) outliers start: 33 outliers final: 20 residues processed: 142 average time/residue: 1.2293 time to fit residues: 187.1202 Evaluate side-chains 148 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 124 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 85 ASN Chi-restraints excluded: chain R residue 111 MET Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 186 MET Chi-restraints excluded: chain R residue 206 SER Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 265 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.7980 chunk 105 optimal weight: 0.0870 chunk 108 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 0.0870 chunk 104 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10169 Z= 0.140 Angle : 0.470 8.904 13751 Z= 0.245 Chirality : 0.038 0.147 1615 Planarity : 0.004 0.046 1660 Dihedral : 7.577 59.958 1817 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.08 % Allowed : 15.25 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.24), residues: 1203 helix: 2.68 (0.19), residues: 666 sheet: 1.07 (0.40), residues: 158 loop : -0.79 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 87 HIS 0.003 0.001 HIS B 147 PHE 0.010 0.001 PHE A 189 TYR 0.011 0.001 TYR P 1 ARG 0.007 0.000 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 1.230 Fit side-chains REVERT: R 45 SER cc_start: 0.6104 (p) cc_final: 0.5870 (t) REVERT: A 17 LYS cc_start: 0.6823 (mttm) cc_final: 0.6484 (mttp) REVERT: B 47 ARG cc_start: 0.6360 (mmm-85) cc_final: 0.5855 (mmt90) REVERT: B 134 ARG cc_start: 0.6216 (ptp-170) cc_final: 0.5838 (tpt170) REVERT: B 217 ASP cc_start: 0.7599 (t0) cc_final: 0.7286 (t0) REVERT: B 222 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.6793 (pmm) REVERT: B 224 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.7025 (mpt180) REVERT: C 21 MET cc_start: 0.5850 (mmm) cc_final: 0.5222 (ptm) REVERT: D 155 LYS cc_start: 0.6702 (mttm) cc_final: 0.6454 (mttp) REVERT: D 158 ASP cc_start: 0.5977 (m-30) cc_final: 0.5769 (m-30) REVERT: D 199 MET cc_start: 0.6924 (ptp) cc_final: 0.6481 (ptt) outliers start: 22 outliers final: 13 residues processed: 143 average time/residue: 1.2162 time to fit residues: 187.0343 Evaluate side-chains 142 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 206 SER Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain D residue 265 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10169 Z= 0.192 Angle : 0.520 9.223 13751 Z= 0.271 Chirality : 0.039 0.145 1615 Planarity : 0.004 0.046 1660 Dihedral : 7.829 58.506 1817 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.89 % Allowed : 15.44 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.99 (0.24), residues: 1203 helix: 2.53 (0.19), residues: 666 sheet: 1.05 (0.40), residues: 158 loop : -0.84 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 87 HIS 0.004 0.001 HIS B 147 PHE 0.020 0.002 PHE R 320 TYR 0.017 0.001 TYR A 230 ARG 0.007 0.001 ARG B 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 124 time to evaluate : 1.158 Fit side-chains REVERT: R 45 SER cc_start: 0.6189 (p) cc_final: 0.5929 (t) REVERT: A 17 LYS cc_start: 0.6886 (mttm) cc_final: 0.6533 (mttp) REVERT: A 269 ASN cc_start: 0.7490 (m-40) cc_final: 0.7208 (m110) REVERT: B 47 ARG cc_start: 0.6303 (mmm-85) cc_final: 0.5816 (mmt90) REVERT: B 134 ARG cc_start: 0.6237 (ptp-170) cc_final: 0.5878 (tpt170) REVERT: B 217 ASP cc_start: 0.7611 (t0) cc_final: 0.7223 (t0) REVERT: B 222 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.6813 (pmm) REVERT: B 224 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.7003 (mpt180) REVERT: C 21 MET cc_start: 0.5844 (mmm) cc_final: 0.5152 (ptm) REVERT: D 155 LYS cc_start: 0.6814 (mttm) cc_final: 0.6555 (mttp) REVERT: D 158 ASP cc_start: 0.6022 (m-30) cc_final: 0.5808 (m-30) REVERT: D 199 MET cc_start: 0.6961 (ptp) cc_final: 0.6519 (ptt) outliers start: 20 outliers final: 15 residues processed: 136 average time/residue: 1.2499 time to fit residues: 182.2744 Evaluate side-chains 140 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 206 SER Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain D residue 265 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 85 optimal weight: 7.9990 chunk 13 optimal weight: 0.1980 chunk 25 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.166359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.128152 restraints weight = 10860.238| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.91 r_work: 0.3182 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10169 Z= 0.209 Angle : 0.530 9.431 13751 Z= 0.277 Chirality : 0.039 0.145 1615 Planarity : 0.004 0.047 1660 Dihedral : 8.073 59.484 1817 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.99 % Allowed : 15.25 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.92 (0.24), residues: 1203 helix: 2.47 (0.19), residues: 666 sheet: 1.04 (0.40), residues: 158 loop : -0.87 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 87 HIS 0.004 0.001 HIS B 147 PHE 0.012 0.002 PHE B 227 TYR 0.021 0.002 TYR A 230 ARG 0.007 0.001 ARG B 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3893.58 seconds wall clock time: 69 minutes 28.35 seconds (4168.35 seconds total)