Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 05:54:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7w_28911/04_2023/8f7w_28911_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7w_28911/04_2023/8f7w_28911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7w_28911/04_2023/8f7w_28911.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7w_28911/04_2023/8f7w_28911.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7w_28911/04_2023/8f7w_28911_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7w_28911/04_2023/8f7w_28911_updated.pdb" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.008 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 5822 2.51 5 N 1511 2.21 5 O 1688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 202": "NH1" <-> "NH2" Residue "R ARG 263": "NH1" <-> "NH2" Residue "R ARG 270": "NH1" <-> "NH2" Residue "P ARG 214": "NH1" <-> "NH2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "A ARG 32": "NH1" <-> "NH2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "E PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 87": "NH1" <-> "NH2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 9087 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2277 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain: "P" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 69 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "A" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1826 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 224} Chain breaks: 1 Chain: "B" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2576 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 329} Chain: "C" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 427 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "E" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1792 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Chain: "R" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 120 Unusual residues: {'CLR': 3, 'PLM': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 5.38, per 1000 atoms: 0.59 Number of scatterers: 9087 At special positions: 0 Unit cell: (104.958, 112.455, 133.875, 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 1688 8.00 N 1511 7.00 C 5822 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 210 " 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: 3.41 Conformation dependent library (CDL) restraints added in 1.5 seconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 14 sheets defined 34.4% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'R' and resid 58 through 85 Processing helix chain 'R' and resid 93 through 121 removed outlier: 3.733A pdb=" N THR R 110 " --> pdb=" O ALA R 106 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR R 111 " --> pdb=" O LEU R 107 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N MET R 112 " --> pdb=" O VAL R 108 " (cutoff:3.500A) Proline residue: R 113 - end of helix Processing helix chain 'R' and resid 128 through 161 Processing helix chain 'R' and resid 163 through 167 removed outlier: 3.657A pdb=" N LEU R 167 " --> pdb=" O PRO R 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 163 through 167' Processing helix chain 'R' and resid 172 through 196 removed outlier: 3.635A pdb=" N SER R 188 " --> pdb=" O LEU R 184 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL R 189 " --> pdb=" O LEU R 185 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 255 removed outlier: 3.756A pdb=" N TYR R 219 " --> pdb=" O ASP R 216 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N SER R 220 " --> pdb=" O ASP R 217 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP R 221 " --> pdb=" O ASP R 218 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TRP R 222 " --> pdb=" O TYR R 219 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP R 223 " --> pdb=" O SER R 220 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE R 225 " --> pdb=" O TRP R 222 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL R 230 " --> pdb=" O LYS R 227 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE R 232 " --> pdb=" O CYS R 229 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE R 233 " --> pdb=" O VAL R 230 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA R 234 " --> pdb=" O PHE R 231 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N VAL R 236 " --> pdb=" O PHE R 233 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE R 237 " --> pdb=" O ALA R 234 " (cutoff:3.500A) Proline residue: R 238 - end of helix removed outlier: 3.614A pdb=" N CYS R 245 " --> pdb=" O ILE R 242 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR R 246 " --> pdb=" O ILE R 243 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU R 248 " --> pdb=" O CYS R 245 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU R 251 " --> pdb=" O LEU R 248 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS R 254 " --> pdb=" O LEU R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 299 Proline residue: R 289 - end of helix Processing helix chain 'R' and resid 306 through 330 removed outlier: 3.775A pdb=" N SER R 323 " --> pdb=" O GLY R 319 " (cutoff:3.500A) Proline residue: R 327 - end of helix Processing helix chain 'R' and resid 335 through 341 removed outlier: 3.765A pdb=" N ARG R 339 " --> pdb=" O GLU R 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 31 removed outlier: 3.963A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 54 Processing helix chain 'A' and resid 209 through 215 removed outlier: 4.296A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 209 through 215' Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.982A 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 8 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.092A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 23 Processing helix chain 'C' and resid 30 through 43 removed outlier: 3.822A pdb=" N TYR C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 222 through 224 No H-bonds generated for 'chain 'E' and resid 222 through 224' Processing sheet with id= A, first strand: chain 'R' and resid 197 through 202 Processing sheet with id= B, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.886A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.833A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.000A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 150 removed outlier: 6.934A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 220 through 222 removed outlier: 3.821A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.693A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.787A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.976A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.612A pdb=" N SER E 71 " --> pdb=" O PHE E 80 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 115 through 117 removed outlier: 3.605A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 141 through 143 removed outlier: 3.711A pdb=" N PHE E 213 " --> pdb=" O CYS E 160 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 147 through 149 removed outlier: 6.954A pdb=" N LYS E 245 " --> pdb=" O VAL E 148 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'E' and resid 227 through 232 removed outlier: 3.909A pdb=" N ILE E 190 " --> pdb=" O TRP E 177 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU E 179 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LEU E 188 " --> pdb=" O LEU E 179 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1083 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: 2.66 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2865 1.34 - 1.46: 1935 1.46 - 1.58: 4378 1.58 - 1.69: 1 1.69 - 1.81: 96 Bond restraints: 9275 Sorted by residual: bond pdb=" C ILE R 237 " pdb=" N PRO R 238 " ideal model delta sigma weight residual 1.335 1.363 -0.028 1.36e-02 5.41e+03 4.09e+00 bond pdb=" C ILE R 58 " pdb=" N PRO R 59 " ideal model delta sigma weight residual 1.336 1.359 -0.024 1.23e-02 6.61e+03 3.75e+00 bond pdb=" CA THR R 288 " pdb=" C THR R 288 " ideal model delta sigma weight residual 1.522 1.546 -0.024 1.26e-02 6.30e+03 3.56e+00 bond pdb=" CA VAL R 207 " pdb=" CB VAL R 207 " ideal model delta sigma weight residual 1.546 1.578 -0.032 1.75e-02 3.27e+03 3.44e+00 bond pdb=" C THR R 288 " pdb=" N PRO R 289 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.41e+00 ... (remaining 9270 not shown) Histogram of bond angle deviations from ideal: 99.59 - 106.51: 210 106.51 - 113.42: 5108 113.42 - 120.33: 3464 120.33 - 127.24: 3700 127.24 - 134.15: 85 Bond angle restraints: 12567 Sorted by residual: angle pdb=" CA ARG E 219 " pdb=" CB ARG E 219 " pdb=" CG ARG E 219 " ideal model delta sigma weight residual 114.10 122.80 -8.70 2.00e+00 2.50e-01 1.89e+01 angle pdb=" C ARG E 192 " pdb=" N MET E 193 " pdb=" CA MET E 193 " ideal model delta sigma weight residual 125.02 131.16 -6.14 1.76e+00 3.23e-01 1.22e+01 angle pdb=" CA ARG A 32 " pdb=" CB ARG A 32 " pdb=" CG ARG A 32 " ideal model delta sigma weight residual 114.10 120.37 -6.27 2.00e+00 2.50e-01 9.83e+00 angle pdb=" C MET R 121 " pdb=" N ASN R 122 " pdb=" CA ASN R 122 " ideal model delta sigma weight residual 124.31 129.53 -5.22 1.67e+00 3.59e-01 9.78e+00 angle pdb=" C TYR R 139 " pdb=" N TYR R 140 " pdb=" CA TYR R 140 " ideal model delta sigma weight residual 120.79 124.99 -4.20 1.39e+00 5.18e-01 9.13e+00 ... (remaining 12562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.18: 5273 14.18 - 28.36: 176 28.36 - 42.53: 37 42.53 - 56.71: 3 56.71 - 70.89: 1 Dihedral angle restraints: 5490 sinusoidal: 2166 harmonic: 3324 Sorted by residual: dihedral pdb=" C ILE R 58 " pdb=" N ILE R 58 " pdb=" CA ILE R 58 " pdb=" CB ILE R 58 " ideal model delta harmonic sigma weight residual -122.00 -131.61 9.61 0 2.50e+00 1.60e-01 1.48e+01 dihedral pdb=" CA HIS B 266 " pdb=" C HIS B 266 " pdb=" N ASP B 267 " pdb=" CA ASP B 267 " ideal model delta harmonic sigma weight residual -180.00 -160.95 -19.05 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 161.89 18.11 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 5487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1290 0.089 - 0.177: 138 0.177 - 0.266: 7 0.266 - 0.355: 3 0.355 - 0.443: 4 Chirality restraints: 1442 Sorted by residual: chirality pdb=" CB ILE R 58 " pdb=" CA ILE R 58 " pdb=" CG1 ILE R 58 " pdb=" CG2 ILE R 58 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.91e+00 chirality pdb=" C14 CLR R 403 " pdb=" C13 CLR R 403 " pdb=" C15 CLR R 403 " pdb=" C8 CLR R 403 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.43 2.00e-01 2.50e+01 4.56e+00 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 -2.74 0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 1439 not shown) Planarity restraints: 1563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER R 220 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.19e+00 pdb=" C SER R 220 " 0.046 2.00e-02 2.50e+03 pdb=" O SER R 220 " -0.017 2.00e-02 2.50e+03 pdb=" N TRP R 221 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 232 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C ILE R 232 " -0.038 2.00e-02 2.50e+03 pdb=" O ILE R 232 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE R 233 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS E 35 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.74e+00 pdb=" C HIS E 35 " 0.038 2.00e-02 2.50e+03 pdb=" O HIS E 35 " -0.014 2.00e-02 2.50e+03 pdb=" N TRP E 36 " -0.013 2.00e-02 2.50e+03 ... (remaining 1560 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2235 2.81 - 3.33: 7839 3.33 - 3.85: 14449 3.85 - 4.38: 16585 4.38 - 4.90: 29346 Nonbonded interactions: 70454 Sorted by model distance: nonbonded pdb=" O ALA R 317 " pdb=" OG1 THR R 321 " model vdw 2.282 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.318 2.440 nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.326 2.440 nonbonded pdb=" O ILE B 123 " pdb=" OG SER B 136 " model vdw 2.358 2.440 nonbonded pdb=" O ILE E 139 " pdb=" OG1 THR E 239 " model vdw 2.361 2.440 ... (remaining 70449 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.690 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 26.190 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 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 0.060 9275 Z= 0.254 Angle : 0.800 9.154 12567 Z= 0.443 Chirality : 0.059 0.443 1442 Planarity : 0.006 0.051 1563 Dihedral : 8.056 70.889 3343 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.80 (0.21), residues: 1129 helix: -0.66 (0.22), residues: 399 sheet: -0.83 (0.29), residues: 287 loop : -1.80 (0.24), residues: 443 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 239 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 240 average time/residue: 0.2514 time to fit residues: 80.0301 Evaluate side-chains 170 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.043 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 0.1980 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 141 ASN R 179 ASN R 322 ASN B 75 GLN B 266 HIS E 232 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 9275 Z= 0.238 Angle : 0.540 7.120 12567 Z= 0.283 Chirality : 0.042 0.209 1442 Planarity : 0.004 0.031 1563 Dihedral : 4.370 36.363 1297 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.65 (0.23), residues: 1129 helix: 0.62 (0.25), residues: 399 sheet: -0.67 (0.28), residues: 289 loop : -1.12 (0.27), residues: 441 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 178 time to evaluate : 1.105 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 20 residues processed: 188 average time/residue: 0.2249 time to fit residues: 57.7581 Evaluate side-chains 169 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 149 time to evaluate : 1.043 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.0889 time to fit residues: 4.7633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.2980 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 89 optimal weight: 0.0170 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.4422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 115 GLN A 304 GLN E 232 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9275 Z= 0.219 Angle : 0.510 6.342 12567 Z= 0.265 Chirality : 0.042 0.211 1442 Planarity : 0.003 0.045 1563 Dihedral : 4.256 29.757 1297 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.03 (0.24), residues: 1129 helix: 1.44 (0.26), residues: 386 sheet: -0.53 (0.28), residues: 295 loop : -0.76 (0.28), residues: 448 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 159 time to evaluate : 0.925 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 169 average time/residue: 0.2317 time to fit residues: 53.4405 Evaluate side-chains 149 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 142 time to evaluate : 0.999 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0838 time to fit residues: 2.5160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 101 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 60 optimal weight: 0.0770 overall best weight: 2.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 9275 Z= 0.381 Angle : 0.604 9.328 12567 Z= 0.313 Chirality : 0.045 0.191 1442 Planarity : 0.004 0.034 1563 Dihedral : 4.946 31.789 1297 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.10 (0.24), residues: 1129 helix: 1.27 (0.26), residues: 387 sheet: -0.71 (0.28), residues: 309 loop : -0.66 (0.29), residues: 433 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 154 time to evaluate : 1.091 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 17 residues processed: 164 average time/residue: 0.2335 time to fit residues: 52.0054 Evaluate side-chains 156 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 139 time to evaluate : 1.043 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0856 time to fit residues: 4.0324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 9275 Z= 0.257 Angle : 0.548 10.985 12567 Z= 0.279 Chirality : 0.043 0.226 1442 Planarity : 0.003 0.032 1563 Dihedral : 4.699 33.310 1297 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.07 (0.24), residues: 1129 helix: 1.44 (0.26), residues: 386 sheet: -0.61 (0.29), residues: 300 loop : -0.61 (0.28), residues: 443 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 146 time to evaluate : 1.056 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 153 average time/residue: 0.2394 time to fit residues: 49.4445 Evaluate side-chains 144 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 134 time to evaluate : 1.066 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1457 time to fit residues: 3.8409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.0020 chunk 26 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 9275 Z= 0.158 Angle : 0.488 7.669 12567 Z= 0.251 Chirality : 0.041 0.216 1442 Planarity : 0.003 0.031 1563 Dihedral : 4.349 28.725 1297 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.33 (0.25), residues: 1129 helix: 1.59 (0.26), residues: 399 sheet: -0.44 (0.28), residues: 304 loop : -0.48 (0.29), residues: 426 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 158 time to evaluate : 1.315 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 160 average time/residue: 0.2346 time to fit residues: 51.1149 Evaluate side-chains 148 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 141 time to evaluate : 1.055 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0857 time to fit residues: 2.4169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 0.0670 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 9275 Z= 0.151 Angle : 0.495 8.846 12567 Z= 0.250 Chirality : 0.040 0.188 1442 Planarity : 0.003 0.031 1563 Dihedral : 4.163 29.511 1297 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.25), residues: 1129 helix: 1.76 (0.26), residues: 400 sheet: -0.38 (0.28), residues: 308 loop : -0.31 (0.30), residues: 421 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 146 time to evaluate : 1.133 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 148 average time/residue: 0.2406 time to fit residues: 48.5103 Evaluate side-chains 142 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 1.010 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0818 time to fit residues: 1.5561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 0.0270 chunk 9 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.8042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 9275 Z= 0.154 Angle : 0.494 10.471 12567 Z= 0.250 Chirality : 0.040 0.194 1442 Planarity : 0.003 0.031 1563 Dihedral : 4.066 29.713 1297 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.25), residues: 1129 helix: 1.79 (0.26), residues: 401 sheet: -0.35 (0.28), residues: 303 loop : -0.24 (0.30), residues: 425 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 149 time to evaluate : 1.034 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 152 average time/residue: 0.2457 time to fit residues: 50.4083 Evaluate side-chains 150 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 144 time to evaluate : 1.005 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0819 time to fit residues: 2.3272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 0.0030 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 105 optimal weight: 0.0970 chunk 64 optimal weight: 0.0980 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 95 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN E 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 9275 Z= 0.123 Angle : 0.487 11.036 12567 Z= 0.246 Chirality : 0.040 0.205 1442 Planarity : 0.003 0.030 1563 Dihedral : 3.906 30.361 1297 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.76 (0.25), residues: 1129 helix: 1.91 (0.26), residues: 401 sheet: -0.24 (0.28), residues: 302 loop : -0.18 (0.30), residues: 426 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.048 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2433 time to fit residues: 48.2064 Evaluate side-chains 141 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.069 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 95 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN E 39 GLN E 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 9275 Z= 0.275 Angle : 0.566 11.123 12567 Z= 0.287 Chirality : 0.043 0.202 1442 Planarity : 0.003 0.031 1563 Dihedral : 4.390 28.674 1297 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.25), residues: 1129 helix: 1.78 (0.26), residues: 395 sheet: -0.37 (0.28), residues: 312 loop : -0.22 (0.30), residues: 422 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 1.083 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 136 average time/residue: 0.2594 time to fit residues: 47.5118 Evaluate side-chains 132 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 129 time to evaluate : 1.110 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0890 time to fit residues: 2.0774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.0040 chunk 13 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.175780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.135027 restraints weight = 10622.113| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.50 r_work: 0.3236 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 9275 Z= 0.156 Angle : 0.516 11.453 12567 Z= 0.262 Chirality : 0.041 0.210 1442 Planarity : 0.003 0.030 1563 Dihedral : 4.130 30.166 1297 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.69 (0.25), residues: 1129 helix: 1.79 (0.26), residues: 401 sheet: -0.26 (0.28), residues: 317 loop : -0.15 (0.31), residues: 411 =============================================================================== Job complete usr+sys time: 2287.30 seconds wall clock time: 42 minutes 14.06 seconds (2534.06 seconds total)