Starting phenix.real_space_refine on Thu Mar 14 14:58:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7w_28911/03_2024/8f7w_28911_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7w_28911/03_2024/8f7w_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_28911/03_2024/8f7w_28911.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7w_28911/03_2024/8f7w_28911.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7w_28911/03_2024/8f7w_28911_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7w_28911/03_2024/8f7w_28911_updated.pdb" } resolution = 3.19 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= 0.008 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-dev-5265/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: 5.14, per 1000 atoms: 0.57 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 1.9 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: 1.90 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: 2.71 Time building geometry restraints manager: 3.75 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: 5423 14.18 - 28.36: 186 28.36 - 42.53: 39 42.53 - 56.71: 9 56.71 - 70.89: 1 Dihedral angle restraints: 5658 sinusoidal: 2334 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 5655 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.280 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.310 Find NCS groups from input model: 0.270 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.370 ------------------------------------------------------------------------------- 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 : 8.286 70.889 3511 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 % Allowed : 0.91 % Favored : 98.99 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 111 HIS 0.004 0.001 HIS E 35 PHE 0.024 0.002 PHE A 189 TYR 0.025 0.002 TYR E 50 ARG 0.006 0.000 ARG B 68 *********************** 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 : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 180 ILE cc_start: 0.6785 (OUTLIER) cc_final: 0.6569 (mp) REVERT: R 297 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7401 (mt-10) REVERT: A 337 ASP cc_start: 0.7854 (m-30) cc_final: 0.7607 (m-30) REVERT: B 211 TRP cc_start: 0.8414 (m100) cc_final: 0.8062 (m100) REVERT: C 41 CYS cc_start: 0.7950 (m) cc_final: 0.7490 (m) outliers start: 1 outliers final: 0 residues processed: 240 average time/residue: 0.2478 time to fit residues: 78.5199 Evaluate side-chains 171 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 170 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 180 ILE 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: 0.7502 moved from start: 0.2561 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= 0.244 Angle : 0.545 7.118 12567 Z= 0.285 Chirality : 0.043 0.188 1442 Planarity : 0.004 0.032 1563 Dihedral : 5.536 43.182 1467 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.43 % Allowed : 6.59 % Favored : 90.98 % 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: -0.62 (0.23), residues: 1129 helix: 0.66 (0.25), residues: 399 sheet: -0.68 (0.28), residues: 289 loop : -1.11 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 111 HIS 0.004 0.001 HIS B 142 PHE 0.021 0.002 PHE B 199 TYR 0.017 0.002 TYR R 140 ARG 0.005 0.001 ARG B 134 *********************** 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 200 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 176 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: R 297 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7269 (mt-10) REVERT: A 33 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7403 (mt-10) REVERT: A 232 LEU cc_start: 0.8145 (mt) cc_final: 0.7923 (mp) REVERT: B 45 MET cc_start: 0.8646 (mtt) cc_final: 0.8407 (mtp) REVERT: B 152 LEU cc_start: 0.8958 (mt) cc_final: 0.8687 (mt) REVERT: B 153 ASP cc_start: 0.7522 (m-30) cc_final: 0.7216 (m-30) REVERT: B 247 ASP cc_start: 0.6782 (t0) cc_final: 0.6506 (t0) REVERT: E 93 MET cc_start: 0.7801 (ttm) cc_final: 0.7541 (ttt) outliers start: 24 outliers final: 21 residues processed: 189 average time/residue: 0.2161 time to fit residues: 55.6773 Evaluate side-chains 167 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 146 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 218 ASP Chi-restraints excluded: chain R residue 266 ASP Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 301 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 239 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 89 optimal weight: 0.3980 chunk 34 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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: 0.7567 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9275 Z= 0.236 Angle : 0.520 6.870 12567 Z= 0.270 Chirality : 0.042 0.194 1442 Planarity : 0.003 0.040 1563 Dihedral : 5.163 41.705 1465 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.94 % Allowed : 8.11 % Favored : 88.96 % 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: -0.12 (0.24), residues: 1129 helix: 1.26 (0.26), residues: 391 sheet: -0.61 (0.28), residues: 296 loop : -0.81 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 99 HIS 0.004 0.001 HIS E 233 PHE 0.013 0.002 PHE B 235 TYR 0.014 0.002 TYR R 140 ARG 0.005 0.000 ARG A 24 *********************** 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 182 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 153 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8187 (mt) cc_final: 0.7942 (mp) REVERT: B 61 MET cc_start: 0.8581 (ppp) cc_final: 0.8293 (ppp) REVERT: B 153 ASP cc_start: 0.7666 (m-30) cc_final: 0.7400 (m-30) REVERT: B 247 ASP cc_start: 0.7124 (t0) cc_final: 0.6883 (t0) REVERT: C 21 MET cc_start: 0.7838 (tpp) cc_final: 0.7607 (tpp) REVERT: C 41 CYS cc_start: 0.8125 (m) cc_final: 0.7847 (m) REVERT: E 46 GLU cc_start: 0.7218 (tt0) cc_final: 0.6936 (tt0) REVERT: E 93 MET cc_start: 0.7885 (ttm) cc_final: 0.7632 (ttt) REVERT: E 161 ARG cc_start: 0.7147 (tpp-160) cc_final: 0.6726 (tpp-160) outliers start: 29 outliers final: 21 residues processed: 172 average time/residue: 0.2146 time to fit residues: 50.3311 Evaluate side-chains 159 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 138 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 171 THR Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 218 ASP Chi-restraints excluded: chain R residue 243 ILE Chi-restraints excluded: chain R residue 266 ASP Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 239 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 9275 Z= 0.464 Angle : 0.645 10.519 12567 Z= 0.334 Chirality : 0.047 0.180 1442 Planarity : 0.004 0.035 1563 Dihedral : 5.885 35.984 1465 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.65 % Allowed : 10.03 % Favored : 86.32 % 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: -0.37 (0.24), residues: 1129 helix: 0.97 (0.25), residues: 393 sheet: -0.82 (0.28), residues: 308 loop : -0.81 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 221 HIS 0.009 0.002 HIS B 54 PHE 0.025 0.002 PHE R 143 TYR 0.020 0.002 TYR E 94 ARG 0.005 0.001 ARG B 314 *********************** 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 180 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 144 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8019 (mt) cc_final: 0.7683 (mp) REVERT: B 19 ARG cc_start: 0.6553 (ttp-170) cc_final: 0.5496 (mtm180) REVERT: B 153 ASP cc_start: 0.7906 (m-30) cc_final: 0.7512 (m-30) REVERT: B 247 ASP cc_start: 0.7351 (t0) cc_final: 0.7068 (t0) REVERT: E 46 GLU cc_start: 0.7540 (tt0) cc_final: 0.7274 (tt0) REVERT: E 93 MET cc_start: 0.7928 (ttm) cc_final: 0.7709 (ttt) outliers start: 36 outliers final: 30 residues processed: 171 average time/residue: 0.2265 time to fit residues: 52.6349 Evaluate side-chains 166 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 171 THR Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 218 ASP Chi-restraints excluded: chain R residue 243 ILE Chi-restraints excluded: chain R residue 247 THR Chi-restraints excluded: chain R residue 266 ASP Chi-restraints excluded: chain R residue 273 THR Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 239 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN E 82 GLN E 232 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9275 Z= 0.190 Angle : 0.519 11.419 12567 Z= 0.264 Chirality : 0.042 0.191 1442 Planarity : 0.003 0.032 1563 Dihedral : 5.365 40.743 1465 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.74 % Allowed : 11.85 % Favored : 85.41 % 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: 0.08 (0.25), residues: 1129 helix: 1.45 (0.26), residues: 392 sheet: -0.56 (0.28), residues: 305 loop : -0.66 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.002 0.001 HIS B 54 PHE 0.014 0.001 PHE R 293 TYR 0.012 0.001 TYR R 140 ARG 0.004 0.000 ARG R 156 *********************** 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 176 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 149 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: R 62 ILE cc_start: 0.6726 (mm) cc_final: 0.6495 (tt) REVERT: R 233 PHE cc_start: 0.8157 (m-80) cc_final: 0.7920 (m-80) REVERT: A 232 LEU cc_start: 0.8006 (mt) cc_final: 0.7643 (mp) REVERT: B 153 ASP cc_start: 0.7571 (m-30) cc_final: 0.7234 (m-30) REVERT: B 214 ARG cc_start: 0.8057 (mmt90) cc_final: 0.7850 (mmt90) REVERT: B 247 ASP cc_start: 0.7198 (t0) cc_final: 0.6961 (t0) REVERT: E 22 CYS cc_start: 0.8209 (t) cc_final: 0.7962 (t) REVERT: E 46 GLU cc_start: 0.7353 (tt0) cc_final: 0.7044 (tt0) outliers start: 27 outliers final: 23 residues processed: 167 average time/residue: 0.2320 time to fit residues: 52.6927 Evaluate side-chains 167 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 144 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 218 ASP Chi-restraints excluded: chain R residue 243 ILE Chi-restraints excluded: chain R residue 266 ASP Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 232 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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: 0.7595 moved from start: 0.4011 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= 0.162 Angle : 0.485 7.831 12567 Z= 0.250 Chirality : 0.041 0.195 1442 Planarity : 0.003 0.031 1563 Dihedral : 5.133 37.480 1465 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.84 % Allowed : 12.77 % Favored : 84.40 % 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: 0.28 (0.25), residues: 1129 helix: 1.60 (0.26), residues: 399 sheet: -0.47 (0.28), residues: 305 loop : -0.56 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 258 HIS 0.003 0.001 HIS E 233 PHE 0.013 0.001 PHE R 293 TYR 0.012 0.001 TYR R 140 ARG 0.004 0.000 ARG B 197 *********************** 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 179 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 151 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: R 62 ILE cc_start: 0.6789 (mm) cc_final: 0.6547 (tt) REVERT: R 233 PHE cc_start: 0.8121 (m-80) cc_final: 0.7910 (m-80) REVERT: A 232 LEU cc_start: 0.8048 (mt) cc_final: 0.7692 (mp) REVERT: A 315 ASP cc_start: 0.7324 (OUTLIER) cc_final: 0.7079 (m-30) REVERT: B 153 ASP cc_start: 0.7568 (m-30) cc_final: 0.7324 (m-30) REVERT: B 247 ASP cc_start: 0.7185 (t0) cc_final: 0.6929 (t0) REVERT: E 46 GLU cc_start: 0.7315 (tt0) cc_final: 0.7041 (tt0) REVERT: E 161 ARG cc_start: 0.7037 (tpp-160) cc_final: 0.6677 (tpp-160) outliers start: 28 outliers final: 26 residues processed: 167 average time/residue: 0.2187 time to fit residues: 50.0521 Evaluate side-chains 171 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 144 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 171 THR Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 218 ASP Chi-restraints excluded: chain R residue 243 ILE Chi-restraints excluded: chain R residue 266 ASP Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 221 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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: 0.7591 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9275 Z= 0.167 Angle : 0.487 9.063 12567 Z= 0.249 Chirality : 0.041 0.197 1442 Planarity : 0.003 0.031 1563 Dihedral : 4.994 35.693 1465 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.44 % Allowed : 12.56 % Favored : 83.99 % 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: 0.46 (0.25), residues: 1129 helix: 1.76 (0.26), residues: 399 sheet: -0.43 (0.28), residues: 305 loop : -0.41 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 99 HIS 0.002 0.001 HIS R 291 PHE 0.011 0.001 PHE R 293 TYR 0.013 0.001 TYR R 119 ARG 0.004 0.000 ARG B 197 *********************** 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 180 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 146 time to evaluate : 1.076 Fit side-chains REVERT: R 62 ILE cc_start: 0.6801 (mm) cc_final: 0.6558 (tt) REVERT: R 233 PHE cc_start: 0.8117 (m-80) cc_final: 0.7916 (m-80) REVERT: A 232 LEU cc_start: 0.8030 (mt) cc_final: 0.7657 (mp) REVERT: A 315 ASP cc_start: 0.7367 (OUTLIER) cc_final: 0.7129 (m-30) REVERT: A 329 THR cc_start: 0.7376 (OUTLIER) cc_final: 0.7134 (p) REVERT: B 19 ARG cc_start: 0.6501 (ttp-170) cc_final: 0.5627 (mtm180) REVERT: B 153 ASP cc_start: 0.7528 (m-30) cc_final: 0.7303 (m-30) REVERT: B 247 ASP cc_start: 0.7142 (t0) cc_final: 0.6881 (t0) REVERT: E 46 GLU cc_start: 0.7295 (tt0) cc_final: 0.7026 (tt0) REVERT: E 161 ARG cc_start: 0.7079 (tpp-160) cc_final: 0.6718 (tpp-160) outliers start: 34 outliers final: 28 residues processed: 167 average time/residue: 0.2195 time to fit residues: 50.1572 Evaluate side-chains 175 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 145 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 171 THR Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 218 ASP Chi-restraints excluded: chain R residue 243 ILE Chi-restraints excluded: chain R residue 266 ASP Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 220 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9275 Z= 0.164 Angle : 0.492 10.412 12567 Z= 0.251 Chirality : 0.041 0.198 1442 Planarity : 0.003 0.031 1563 Dihedral : 4.905 33.862 1465 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.24 % Allowed : 13.07 % Favored : 83.69 % 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: 0.48 (0.25), residues: 1129 helix: 1.79 (0.26), residues: 399 sheet: -0.53 (0.28), residues: 305 loop : -0.32 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 99 HIS 0.002 0.001 HIS R 291 PHE 0.010 0.001 PHE R 293 TYR 0.012 0.001 TYR R 140 ARG 0.003 0.000 ARG B 197 *********************** 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 181 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 149 time to evaluate : 1.056 Fit side-chains revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8033 (mt) cc_final: 0.7666 (mp) REVERT: A 329 THR cc_start: 0.7416 (OUTLIER) cc_final: 0.7214 (p) REVERT: B 19 ARG cc_start: 0.6606 (ttp-170) cc_final: 0.5666 (mtm180) REVERT: B 153 ASP cc_start: 0.7517 (m-30) cc_final: 0.7307 (m-30) REVERT: B 247 ASP cc_start: 0.7122 (t0) cc_final: 0.6862 (t0) REVERT: E 46 GLU cc_start: 0.7337 (tt0) cc_final: 0.7068 (tt0) outliers start: 32 outliers final: 27 residues processed: 167 average time/residue: 0.2288 time to fit residues: 51.8407 Evaluate side-chains 176 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 148 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 171 THR Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 218 ASP Chi-restraints excluded: chain R residue 243 ILE Chi-restraints excluded: chain R residue 266 ASP Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 221 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 20.0000 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9275 Z= 0.183 Angle : 0.498 10.759 12567 Z= 0.253 Chirality : 0.041 0.201 1442 Planarity : 0.003 0.031 1563 Dihedral : 4.894 33.180 1465 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.14 % Allowed : 13.37 % Favored : 83.49 % 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: 0.53 (0.25), residues: 1129 helix: 1.82 (0.26), residues: 399 sheet: -0.53 (0.28), residues: 306 loop : -0.27 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 99 HIS 0.002 0.001 HIS E 35 PHE 0.010 0.001 PHE B 199 TYR 0.012 0.001 TYR R 140 ARG 0.003 0.000 ARG B 197 *********************** 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 174 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 143 time to evaluate : 1.093 Fit side-chains REVERT: A 232 LEU cc_start: 0.8032 (mt) cc_final: 0.7684 (mp) REVERT: A 329 THR cc_start: 0.7437 (OUTLIER) cc_final: 0.7201 (p) REVERT: B 19 ARG cc_start: 0.6619 (ttp-170) cc_final: 0.5735 (mtm180) REVERT: B 247 ASP cc_start: 0.7124 (t0) cc_final: 0.6871 (t0) REVERT: E 46 GLU cc_start: 0.7338 (tt0) cc_final: 0.7072 (tt0) outliers start: 31 outliers final: 29 residues processed: 161 average time/residue: 0.2198 time to fit residues: 48.2374 Evaluate side-chains 170 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 140 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 171 THR Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 218 ASP Chi-restraints excluded: chain R residue 243 ILE Chi-restraints excluded: chain R residue 266 ASP Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 221 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9275 Z= 0.299 Angle : 0.558 11.096 12567 Z= 0.284 Chirality : 0.043 0.194 1442 Planarity : 0.003 0.032 1563 Dihedral : 5.263 34.802 1465 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.44 % Allowed : 13.37 % Favored : 83.18 % 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: 0.41 (0.25), residues: 1129 helix: 1.72 (0.26), residues: 393 sheet: -0.62 (0.28), residues: 314 loop : -0.26 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.002 PHE R 143 TYR 0.012 0.002 TYR E 94 ARG 0.003 0.000 ARG B 314 ********************** 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 170 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 136 time to evaluate : 1.052 Fit side-chains REVERT: A 232 LEU cc_start: 0.7962 (mt) cc_final: 0.7562 (mp) REVERT: A 329 THR cc_start: 0.7449 (OUTLIER) cc_final: 0.7207 (p) REVERT: B 247 ASP cc_start: 0.7256 (t0) cc_final: 0.7004 (t0) REVERT: C 38 MET cc_start: 0.6775 (ptm) cc_final: 0.6397 (ptp) REVERT: E 46 GLU cc_start: 0.7356 (tt0) cc_final: 0.7077 (tt0) outliers start: 34 outliers final: 29 residues processed: 156 average time/residue: 0.2392 time to fit residues: 49.9692 Evaluate side-chains 166 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 171 THR Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 218 ASP Chi-restraints excluded: chain R residue 243 ILE Chi-restraints excluded: chain R residue 266 ASP Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 224 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.0070 chunk 13 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 88 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 11 optimal weight: 0.0970 chunk 16 optimal weight: 8.9990 chunk 77 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 95 ASN R 268 ASN E 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.180872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.140773 restraints weight = 10605.159| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.31 r_work: 0.3301 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4295 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= 0.127 Angle : 0.489 11.671 12567 Z= 0.250 Chirality : 0.040 0.206 1442 Planarity : 0.003 0.031 1563 Dihedral : 4.834 36.112 1465 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.23 % Allowed : 14.99 % Favored : 82.78 % 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: 0.60 (0.25), residues: 1129 helix: 1.83 (0.26), residues: 400 sheet: -0.42 (0.28), residues: 317 loop : -0.22 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 287 HIS 0.002 0.000 HIS E 35 PHE 0.011 0.001 PHE R 293 TYR 0.012 0.001 TYR R 140 ARG 0.009 0.000 ARG P 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2318.00 seconds wall clock time: 42 minutes 17.27 seconds (2537.27 seconds total)