Starting phenix.real_space_refine on Sun Jun 8 03:24:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f7w_28911/06_2025/8f7w_28911.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f7w_28911/06_2025/8f7w_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/cci-nas-00/data/ceres_data/8f7w_28911/06_2025/8f7w_28911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f7w_28911/06_2025/8f7w_28911.map" model { file = "/net/cci-nas-00/data/ceres_data/8f7w_28911/06_2025/8f7w_28911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f7w_28911/06_2025/8f7w_28911.cif" } 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. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 5.49, per 1000 atoms: 0.60 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 1.0 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... Secondary structure from input PDB file: 29 helices and 15 sheets defined 38.2% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'R' and resid 57 through 86 Processing helix chain 'R' and resid 92 through 110 removed outlier: 3.787A pdb=" N ILE R 96 " --> pdb=" O THR R 92 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR R 110 " --> pdb=" O ALA R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 122 Processing helix chain 'R' and resid 127 through 162 Processing helix chain 'R' and resid 162 through 168 removed outlier: 3.657A pdb=" N LEU R 167 " --> pdb=" O PRO R 163 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP R 168 " --> pdb=" O VAL R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 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 215 through 217 No H-bonds generated for 'chain 'R' and resid 215 through 217' Processing helix chain 'R' and resid 218 through 255 removed outlier: 4.689A pdb=" N ILE R 237 " --> pdb=" O PHE R 233 " (cutoff:3.500A) Proline residue: R 238 - end of helix removed outlier: 3.738A pdb=" N SER R 255 " --> pdb=" O LEU R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 300 Proline residue: R 289 - end of helix Processing helix chain 'R' and resid 305 through 331 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 334 through 342 removed outlier: 3.765A pdb=" N ARG R 339 " --> pdb=" O GLU R 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 32 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 46 through 55 Processing helix chain 'A' and resid 208 through 213 removed outlier: 4.296A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.501A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.083A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.761A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 29 through 44 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 48 removed outlier: 3.892A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.850A pdb=" N SER E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.118A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 225 removed outlier: 3.714A pdb=" N VAL E 225 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 197 through 202 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.949A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) 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) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.329A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA4, 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: 6.214A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.377A 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=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.145A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.133A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.372A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 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=AB1, 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=AB2, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AB3, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.603A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB4, 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=AB5, first strand: chain 'E' and resid 147 through 149 removed outlier: 3.538A pdb=" N GLU E 247 " --> pdb=" O VAL E 148 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 190 through 191 445 hydrogen bonds defined for protein. 1278 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: 2.51 Time building geometry restraints manager: 2.82 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: 0.00 - 1.83: 12083 1.83 - 3.66: 395 3.66 - 5.49: 66 5.49 - 7.32: 20 7.32 - 9.15: 3 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: 2226 2.81 - 3.33: 7797 3.33 - 3.85: 14396 3.85 - 4.38: 16496 4.38 - 4.90: 29335 Nonbonded interactions: 70250 Sorted by model distance: nonbonded pdb=" O ALA R 317 " pdb=" OG1 THR R 321 " model vdw 2.282 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.318 3.040 nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.326 3.040 nonbonded pdb=" O ILE B 123 " pdb=" OG SER B 136 " model vdw 2.358 3.040 nonbonded pdb=" O ILE E 139 " pdb=" OG1 THR E 239 " model vdw 2.361 3.040 ... (remaining 70245 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.200 Find NCS groups from input model: 0.110 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.020 ------------------------------------------------------------------------------- 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 9276 Z= 0.209 Angle : 0.801 9.154 12569 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 Details of bonding type rmsd hydrogen bonds : bond 0.12925 ( 445) hydrogen bonds : angle 6.39993 ( 1278) SS BOND : bond 0.00558 ( 1) SS BOND : angle 2.33652 ( 2) covalent geometry : bond 0.00383 ( 9275) covalent geometry : angle 0.80006 (12567) *********************** 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 to be fit. rotamer outliers: 1 poor density : 239 time to evaluate : 1.046 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: 0.2565 time to fit residues: 81.2123 Evaluate side-chains 171 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 170 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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: 5.9990 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 141 ASN R 322 ASN B 75 GLN B 266 HIS E 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.180617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.140064 restraints weight = 10371.122| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.35 r_work: 0.3235 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 9276 Z= 0.276 Angle : 0.671 10.103 12569 Z= 0.352 Chirality : 0.047 0.218 1442 Planarity : 0.004 0.034 1563 Dihedral : 5.921 41.327 1467 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.94 % Allowed : 7.09 % Favored : 89.97 % 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: -0.58 (0.23), residues: 1129 helix: 0.85 (0.24), residues: 395 sheet: -0.81 (0.28), residues: 304 loop : -1.10 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP E 111 HIS 0.007 0.002 HIS B 54 PHE 0.020 0.002 PHE B 199 TYR 0.019 0.002 TYR B 264 ARG 0.007 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.05107 ( 445) hydrogen bonds : angle 5.12687 ( 1278) SS BOND : bond 0.00727 ( 1) SS BOND : angle 3.80274 ( 2) covalent geometry : bond 0.00663 ( 9275) covalent geometry : angle 0.66931 (12567) *********************** 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 199 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: R 297 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7123 (mt-10) REVERT: A 232 LEU cc_start: 0.8018 (mt) cc_final: 0.7651 (mp) REVERT: B 45 MET cc_start: 0.8749 (mtt) cc_final: 0.8475 (mtp) REVERT: B 46 ARG cc_start: 0.8461 (mtt180) cc_final: 0.7928 (mtp85) REVERT: B 153 ASP cc_start: 0.8299 (m-30) cc_final: 0.7994 (m-30) REVERT: B 247 ASP cc_start: 0.7579 (t0) cc_final: 0.7291 (t0) REVERT: C 38 MET cc_start: 0.7248 (mtp) cc_final: 0.6997 (mtp) REVERT: E 20 LEU cc_start: 0.8109 (mt) cc_final: 0.7891 (mt) REVERT: E 46 GLU cc_start: 0.8020 (tt0) cc_final: 0.7713 (tt0) REVERT: E 82 GLN cc_start: 0.8218 (mm110) cc_final: 0.8013 (mm110) REVERT: E 161 ARG cc_start: 0.7440 (tpp-160) cc_final: 0.7192 (tpp-160) outliers start: 29 outliers final: 20 residues processed: 188 average time/residue: 0.2811 time to fit residues: 72.2053 Evaluate side-chains 166 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 218 ASP Chi-restraints excluded: chain R residue 228 ILE 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 251 ASP 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 128 THR Chi-restraints excluded: chain B residue 172 GLU 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 218 SER 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 23 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 110 optimal weight: 0.0970 chunk 28 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 88 ASN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.185661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.146604 restraints weight = 10612.495| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.31 r_work: 0.3298 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9276 Z= 0.104 Angle : 0.486 6.281 12569 Z= 0.255 Chirality : 0.041 0.212 1442 Planarity : 0.003 0.033 1563 Dihedral : 5.136 41.890 1465 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.82 % Allowed : 10.13 % Favored : 88.04 % 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: 0.29 (0.25), residues: 1129 helix: 1.71 (0.26), residues: 405 sheet: -0.45 (0.28), residues: 300 loop : -0.72 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 287 HIS 0.004 0.001 HIS B 225 PHE 0.012 0.001 PHE R 293 TYR 0.013 0.001 TYR B 59 ARG 0.004 0.000 ARG R 257 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 445) hydrogen bonds : angle 4.58792 ( 1278) SS BOND : bond 0.00274 ( 1) SS BOND : angle 2.37076 ( 2) covalent geometry : bond 0.00227 ( 9275) covalent geometry : angle 0.48553 (12567) *********************** 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 175 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: R 233 PHE cc_start: 0.8145 (m-80) cc_final: 0.7886 (m-80) REVERT: R 297 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7211 (mt-10) REVERT: A 232 LEU cc_start: 0.7935 (mt) cc_final: 0.7573 (mp) REVERT: A 251 ASP cc_start: 0.7901 (t70) cc_final: 0.7690 (t0) REVERT: A 255 ASN cc_start: 0.7417 (m110) cc_final: 0.7142 (m-40) REVERT: B 46 ARG cc_start: 0.8401 (mtt180) cc_final: 0.7881 (mtp85) REVERT: B 98 SER cc_start: 0.9024 (m) cc_final: 0.8731 (t) REVERT: B 153 ASP cc_start: 0.8126 (m-30) cc_final: 0.7844 (m-30) REVERT: B 247 ASP cc_start: 0.7756 (t0) cc_final: 0.7451 (t0) REVERT: B 334 SER cc_start: 0.8566 (m) cc_final: 0.8309 (t) REVERT: E 46 GLU cc_start: 0.7898 (tt0) cc_final: 0.7588 (tt0) REVERT: E 82 GLN cc_start: 0.8211 (mm110) cc_final: 0.7974 (mm110) REVERT: E 161 ARG cc_start: 0.7272 (tpp-160) cc_final: 0.7007 (tpp-160) outliers start: 18 outliers final: 11 residues processed: 165 average time/residue: 0.2579 time to fit residues: 57.6237 Evaluate side-chains 156 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 ILE 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 266 ASP Chi-restraints excluded: chain R residue 290 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 243 THR 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 20 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 0.0270 chunk 55 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.183428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.143540 restraints weight = 10373.839| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.34 r_work: 0.3454 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9276 Z= 0.129 Angle : 0.501 6.790 12569 Z= 0.261 Chirality : 0.041 0.216 1442 Planarity : 0.003 0.038 1563 Dihedral : 5.034 40.659 1465 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.33 % Allowed : 10.23 % Favored : 87.44 % 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: 0.56 (0.25), residues: 1129 helix: 2.07 (0.26), residues: 399 sheet: -0.36 (0.28), residues: 302 loop : -0.64 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.004 0.001 HIS B 225 PHE 0.012 0.001 PHE B 199 TYR 0.014 0.001 TYR B 59 ARG 0.004 0.000 ARG R 257 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 445) hydrogen bonds : angle 4.43760 ( 1278) SS BOND : bond 0.00343 ( 1) SS BOND : angle 2.31938 ( 2) covalent geometry : bond 0.00302 ( 9275) covalent geometry : angle 0.50035 (12567) *********************** 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 182 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: R 233 PHE cc_start: 0.8111 (m-80) cc_final: 0.7872 (m-80) REVERT: R 297 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7267 (mt-10) REVERT: A 232 LEU cc_start: 0.7999 (mt) cc_final: 0.7627 (mp) REVERT: A 251 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7807 (t0) REVERT: A 329 THR cc_start: 0.7335 (OUTLIER) cc_final: 0.7057 (p) REVERT: B 46 ARG cc_start: 0.8234 (mtt180) cc_final: 0.7933 (mtp85) REVERT: B 153 ASP cc_start: 0.8014 (m-30) cc_final: 0.7781 (m-30) REVERT: B 247 ASP cc_start: 0.7667 (t0) cc_final: 0.7395 (t0) REVERT: B 334 SER cc_start: 0.8420 (m) cc_final: 0.8143 (t) REVERT: E 46 GLU cc_start: 0.7854 (tt0) cc_final: 0.7637 (tt0) REVERT: E 161 ARG cc_start: 0.7296 (tpp-160) cc_final: 0.7071 (tpp-160) outliers start: 23 outliers final: 19 residues processed: 172 average time/residue: 0.2679 time to fit residues: 63.0587 Evaluate side-chains 178 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 171 THR 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 290 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 251 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 37 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain E residue 91 THR 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 24 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 110 optimal weight: 0.0270 chunk 35 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 0.3980 chunk 60 optimal weight: 0.8980 chunk 99 optimal weight: 0.4980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 269 ASN E 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.183327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.138328 restraints weight = 10616.089| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.40 r_work: 0.3344 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9276 Z= 0.093 Angle : 0.469 7.801 12569 Z= 0.242 Chirality : 0.040 0.221 1442 Planarity : 0.003 0.035 1563 Dihedral : 4.807 39.862 1465 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.53 % Allowed : 10.84 % Favored : 86.63 % 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: 0.84 (0.25), residues: 1129 helix: 2.31 (0.26), residues: 404 sheet: -0.23 (0.28), residues: 303 loop : -0.50 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.003 0.001 HIS B 225 PHE 0.010 0.001 PHE A 189 TYR 0.012 0.001 TYR R 140 ARG 0.004 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03223 ( 445) hydrogen bonds : angle 4.24088 ( 1278) SS BOND : bond 0.00352 ( 1) SS BOND : angle 1.91890 ( 2) covalent geometry : bond 0.00201 ( 9275) covalent geometry : angle 0.46858 (12567) *********************** 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 182 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 2.074 Fit side-chains revert: symmetry clash REVERT: R 91 LYS cc_start: 0.7383 (mptt) cc_final: 0.7089 (mmtt) REVERT: R 233 PHE cc_start: 0.8129 (m-80) cc_final: 0.7919 (m-80) REVERT: R 297 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7152 (mt-10) REVERT: R 332 PHE cc_start: 0.5852 (m-10) cc_final: 0.5552 (m-10) REVERT: A 232 LEU cc_start: 0.7762 (mt) cc_final: 0.7318 (mp) REVERT: A 251 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7782 (t0) REVERT: A 306 GLN cc_start: 0.8073 (mt0) cc_final: 0.7779 (mt0) REVERT: A 329 THR cc_start: 0.7413 (OUTLIER) cc_final: 0.7111 (p) REVERT: B 46 ARG cc_start: 0.8345 (mtt180) cc_final: 0.7755 (mtp85) REVERT: B 153 ASP cc_start: 0.7983 (m-30) cc_final: 0.7714 (m-30) REVERT: B 247 ASP cc_start: 0.7816 (t0) cc_final: 0.7518 (t0) REVERT: B 262 MET cc_start: 0.8184 (mtp) cc_final: 0.7974 (mtp) REVERT: E 46 GLU cc_start: 0.7919 (tt0) cc_final: 0.7547 (mt-10) REVERT: E 82 GLN cc_start: 0.8264 (mm110) cc_final: 0.7990 (mm110) REVERT: E 161 ARG cc_start: 0.7254 (tpp-160) cc_final: 0.6967 (tpp-160) outliers start: 25 outliers final: 22 residues processed: 174 average time/residue: 0.4171 time to fit residues: 100.3069 Evaluate side-chains 170 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 1.292 ------------------------------------------------------------------------------- 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 129 VAL Chi-restraints excluded: chain R residue 171 THR 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 251 ASP Chi-restraints excluded: chain A residue 269 ASN 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 172 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR 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 239 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 28 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 86 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 100 ASN R 122 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.183174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.143704 restraints weight = 10470.751| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.38 r_work: 0.3335 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9276 Z= 0.101 Angle : 0.472 8.754 12569 Z= 0.243 Chirality : 0.041 0.222 1442 Planarity : 0.003 0.034 1563 Dihedral : 4.763 38.947 1465 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.84 % Allowed : 11.14 % Favored : 86.02 % 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: 0.99 (0.25), residues: 1129 helix: 2.43 (0.26), residues: 404 sheet: -0.14 (0.29), residues: 292 loop : -0.42 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 111 HIS 0.003 0.001 HIS B 225 PHE 0.010 0.001 PHE A 189 TYR 0.012 0.001 TYR R 140 ARG 0.004 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03249 ( 445) hydrogen bonds : angle 4.16814 ( 1278) SS BOND : bond 0.00370 ( 1) SS BOND : angle 1.99599 ( 2) covalent geometry : bond 0.00225 ( 9275) covalent geometry : angle 0.47127 (12567) *********************** 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 to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: R 91 LYS cc_start: 0.7465 (mptt) cc_final: 0.7134 (mmtt) REVERT: R 233 PHE cc_start: 0.8088 (m-80) cc_final: 0.7859 (m-80) REVERT: R 332 PHE cc_start: 0.6009 (m-10) cc_final: 0.5710 (m-10) REVERT: A 232 LEU cc_start: 0.7909 (mt) cc_final: 0.7486 (mp) REVERT: A 318 GLU cc_start: 0.6463 (mm-30) cc_final: 0.6252 (mm-30) REVERT: A 329 THR cc_start: 0.7348 (OUTLIER) cc_final: 0.7043 (p) REVERT: B 46 ARG cc_start: 0.8156 (mtt180) cc_final: 0.7794 (mtp85) REVERT: B 153 ASP cc_start: 0.7859 (m-30) cc_final: 0.7616 (m-30) REVERT: B 247 ASP cc_start: 0.7740 (t0) cc_final: 0.7468 (t0) REVERT: B 262 MET cc_start: 0.8000 (mtp) cc_final: 0.7783 (mtp) REVERT: E 46 GLU cc_start: 0.7760 (tt0) cc_final: 0.7506 (mt-10) REVERT: E 161 ARG cc_start: 0.7263 (tpp-160) cc_final: 0.6993 (tpp-160) outliers start: 28 outliers final: 21 residues processed: 170 average time/residue: 0.2343 time to fit residues: 53.8576 Evaluate side-chains 165 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 129 VAL Chi-restraints excluded: chain R residue 171 THR 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 269 ASN 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 172 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR 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 239 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 73 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 98 optimal weight: 0.6980 chunk 102 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 52 optimal weight: 0.2980 chunk 35 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 101 optimal weight: 0.0060 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 100 ASN A 269 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 = 0.4171 r_free = 0.4171 target = 0.183210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.143135 restraints weight = 10579.296| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.40 r_work: 0.3217 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9276 Z= 0.126 Angle : 0.499 8.939 12569 Z= 0.257 Chirality : 0.041 0.224 1442 Planarity : 0.003 0.033 1563 Dihedral : 4.866 37.247 1465 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.04 % Allowed : 11.65 % Favored : 85.31 % 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: 1.03 (0.25), residues: 1129 helix: 2.47 (0.26), residues: 403 sheet: -0.15 (0.29), residues: 293 loop : -0.38 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 221 HIS 0.003 0.001 HIS B 225 PHE 0.011 0.001 PHE B 199 TYR 0.012 0.001 TYR B 59 ARG 0.007 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03510 ( 445) hydrogen bonds : angle 4.19427 ( 1278) SS BOND : bond 0.00350 ( 1) SS BOND : angle 2.19130 ( 2) covalent geometry : bond 0.00293 ( 9275) covalent geometry : angle 0.49863 (12567) *********************** 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 187 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 1.135 Fit side-chains REVERT: R 233 PHE cc_start: 0.8186 (m-80) cc_final: 0.7943 (m-80) REVERT: R 332 PHE cc_start: 0.5846 (m-10) cc_final: 0.5542 (m-10) REVERT: A 232 LEU cc_start: 0.7721 (mt) cc_final: 0.7241 (mp) REVERT: A 306 GLN cc_start: 0.8090 (mt0) cc_final: 0.7750 (mm-40) REVERT: A 315 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7455 (m-30) REVERT: A 329 THR cc_start: 0.7347 (OUTLIER) cc_final: 0.7038 (p) REVERT: B 46 ARG cc_start: 0.8329 (mtt180) cc_final: 0.7687 (mtp85) REVERT: B 153 ASP cc_start: 0.8083 (m-30) cc_final: 0.7805 (m-30) REVERT: B 247 ASP cc_start: 0.7865 (t0) cc_final: 0.7549 (t0) REVERT: E 46 GLU cc_start: 0.7966 (tt0) cc_final: 0.7593 (mt-10) REVERT: E 158 ILE cc_start: 0.6962 (OUTLIER) cc_final: 0.6579 (pt) REVERT: E 161 ARG cc_start: 0.7305 (tpp-160) cc_final: 0.6975 (tpp-160) outliers start: 30 outliers final: 23 residues processed: 177 average time/residue: 0.2481 time to fit residues: 59.9222 Evaluate side-chains 175 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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 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 184 ILE Chi-restraints excluded: chain A residue 269 ASN 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 128 THR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR 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 239 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 72 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 259 GLN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.182188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.141987 restraints weight = 10785.806| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.43 r_work: 0.3236 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9276 Z= 0.146 Angle : 0.518 9.548 12569 Z= 0.267 Chirality : 0.042 0.222 1442 Planarity : 0.003 0.033 1563 Dihedral : 4.979 36.516 1465 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.04 % Allowed : 11.55 % 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: 1.02 (0.25), residues: 1129 helix: 2.39 (0.26), residues: 403 sheet: -0.07 (0.29), residues: 296 loop : -0.36 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 258 HIS 0.004 0.001 HIS B 225 PHE 0.014 0.001 PHE R 293 TYR 0.014 0.001 TYR B 59 ARG 0.006 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03639 ( 445) hydrogen bonds : angle 4.23262 ( 1278) SS BOND : bond 0.00363 ( 1) SS BOND : angle 2.36434 ( 2) covalent geometry : bond 0.00345 ( 9275) covalent geometry : angle 0.51721 (12567) *********************** 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 187 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.987 Fit side-chains REVERT: R 233 PHE cc_start: 0.8186 (m-80) cc_final: 0.7955 (m-80) REVERT: R 332 PHE cc_start: 0.5862 (m-10) cc_final: 0.5549 (m-10) REVERT: A 315 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7387 (m-30) REVERT: A 329 THR cc_start: 0.7354 (OUTLIER) cc_final: 0.7043 (p) REVERT: B 46 ARG cc_start: 0.8327 (mtt180) cc_final: 0.7677 (mtp85) REVERT: B 153 ASP cc_start: 0.8133 (m-30) cc_final: 0.7856 (m-30) REVERT: B 213 VAL cc_start: 0.8816 (OUTLIER) cc_final: 0.8470 (m) REVERT: B 217 MET cc_start: 0.7818 (ptm) cc_final: 0.7585 (ptp) REVERT: B 247 ASP cc_start: 0.7894 (t0) cc_final: 0.7612 (t0) REVERT: E 46 GLU cc_start: 0.7951 (tt0) cc_final: 0.7561 (mt-10) REVERT: E 158 ILE cc_start: 0.6996 (OUTLIER) cc_final: 0.6608 (pt) REVERT: E 161 ARG cc_start: 0.7335 (tpp-160) cc_final: 0.7011 (tpp-160) outliers start: 30 outliers final: 23 residues processed: 175 average time/residue: 0.2408 time to fit residues: 57.2896 Evaluate side-chains 180 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 129 VAL Chi-restraints excluded: chain R residue 171 THR Chi-restraints excluded: chain R residue 180 ILE 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 269 ASN Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 213 VAL 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 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 214 THR Chi-restraints excluded: chain E residue 239 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 46 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.179674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.138940 restraints weight = 10662.603| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.46 r_work: 0.3225 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9276 Z= 0.123 Angle : 0.503 9.583 12569 Z= 0.260 Chirality : 0.041 0.223 1442 Planarity : 0.003 0.033 1563 Dihedral : 4.920 35.795 1465 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.74 % Allowed : 12.46 % Favored : 84.80 % 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: 1.08 (0.25), residues: 1129 helix: 2.40 (0.26), residues: 406 sheet: -0.10 (0.29), residues: 298 loop : -0.26 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 258 HIS 0.003 0.001 HIS B 225 PHE 0.013 0.001 PHE R 293 TYR 0.016 0.001 TYR R 119 ARG 0.006 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03496 ( 445) hydrogen bonds : angle 4.17062 ( 1278) SS BOND : bond 0.00389 ( 1) SS BOND : angle 2.22946 ( 2) covalent geometry : bond 0.00284 ( 9275) covalent geometry : angle 0.50270 (12567) *********************** 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 180 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 1.050 Fit side-chains REVERT: R 233 PHE cc_start: 0.8169 (m-80) cc_final: 0.7954 (m-80) REVERT: R 332 PHE cc_start: 0.5834 (m-10) cc_final: 0.5526 (m-10) REVERT: A 306 GLN cc_start: 0.8108 (mt0) cc_final: 0.7781 (mt0) REVERT: A 315 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7420 (m-30) REVERT: A 329 THR cc_start: 0.7355 (OUTLIER) cc_final: 0.7040 (p) REVERT: B 19 ARG cc_start: 0.6435 (ttp-170) cc_final: 0.5539 (mtm180) REVERT: B 46 ARG cc_start: 0.8321 (mtt180) cc_final: 0.7686 (mtp85) REVERT: B 153 ASP cc_start: 0.8096 (m-30) cc_final: 0.7803 (m-30) REVERT: B 247 ASP cc_start: 0.7872 (t0) cc_final: 0.7551 (t0) REVERT: E 46 GLU cc_start: 0.7974 (tt0) cc_final: 0.7502 (mt-10) REVERT: E 161 ARG cc_start: 0.7339 (tpp-160) cc_final: 0.7005 (tpp-160) outliers start: 27 outliers final: 24 residues processed: 169 average time/residue: 0.2446 time to fit residues: 55.5824 Evaluate side-chains 183 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 129 VAL Chi-restraints excluded: chain R residue 171 THR Chi-restraints excluded: chain R residue 180 ILE 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 269 ASN Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 65 THR 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 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 239 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 66 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.4161 r_free = 0.4161 target = 0.182255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.141663 restraints weight = 10646.109| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.29 r_work: 0.3444 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9276 Z= 0.137 Angle : 0.519 10.375 12569 Z= 0.267 Chirality : 0.042 0.222 1442 Planarity : 0.003 0.033 1563 Dihedral : 4.968 35.283 1465 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.14 % Allowed : 12.26 % Favored : 84.60 % 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: 1.06 (0.25), residues: 1129 helix: 2.36 (0.26), residues: 406 sheet: -0.10 (0.29), residues: 298 loop : -0.24 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 258 HIS 0.003 0.001 HIS B 225 PHE 0.014 0.001 PHE R 293 TYR 0.014 0.001 TYR B 59 ARG 0.007 0.000 ARG R 257 Details of bonding type rmsd hydrogen bonds : bond 0.03589 ( 445) hydrogen bonds : angle 4.19160 ( 1278) SS BOND : bond 0.00377 ( 1) SS BOND : angle 2.31825 ( 2) covalent geometry : bond 0.00321 ( 9275) covalent geometry : angle 0.51817 (12567) ********************** 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 189 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.932 Fit side-chains REVERT: R 233 PHE cc_start: 0.8315 (m-80) cc_final: 0.8062 (m-80) REVERT: R 328 ILE cc_start: 0.8671 (tt) cc_final: 0.8425 (tt) REVERT: R 332 PHE cc_start: 0.6123 (m-10) cc_final: 0.5848 (m-10) REVERT: A 298 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8129 (mt-10) REVERT: A 306 GLN cc_start: 0.8182 (mt0) cc_final: 0.7977 (mt0) REVERT: A 315 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7559 (m-30) REVERT: A 329 THR cc_start: 0.7390 (OUTLIER) cc_final: 0.7076 (p) REVERT: B 19 ARG cc_start: 0.6646 (ttp-170) cc_final: 0.5832 (mtm180) REVERT: B 46 ARG cc_start: 0.8463 (mtt180) cc_final: 0.7946 (mtp85) REVERT: B 153 ASP cc_start: 0.8207 (m-30) cc_final: 0.7959 (m-30) REVERT: B 247 ASP cc_start: 0.7975 (t0) cc_final: 0.7720 (t0) REVERT: E 46 GLU cc_start: 0.8015 (tt0) cc_final: 0.7686 (mt-10) REVERT: E 158 ILE cc_start: 0.7199 (OUTLIER) cc_final: 0.6801 (pt) REVERT: E 161 ARG cc_start: 0.7412 (tpp-160) cc_final: 0.7128 (tpp-160) outliers start: 31 outliers final: 23 residues processed: 176 average time/residue: 0.2345 time to fit residues: 55.5279 Evaluate side-chains 180 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 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 184 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 298 GLU 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 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 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 214 THR Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 239 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 3 optimal weight: 0.0040 chunk 72 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 90 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 0.0270 overall best weight: 0.8852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 115 GLN A 269 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 = 0.4168 r_free = 0.4168 target = 0.183057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.142489 restraints weight = 10547.581| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.32 r_work: 0.3468 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9276 Z= 0.111 Angle : 0.500 10.598 12569 Z= 0.257 Chirality : 0.041 0.223 1442 Planarity : 0.003 0.032 1563 Dihedral : 4.847 34.281 1465 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.63 % Allowed : 12.87 % Favored : 84.50 % 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: 1.15 (0.25), residues: 1129 helix: 2.45 (0.26), residues: 407 sheet: -0.06 (0.29), residues: 293 loop : -0.22 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.003 0.001 HIS B 225 PHE 0.014 0.001 PHE R 293 TYR 0.012 0.001 TYR R 140 ARG 0.006 0.000 ARG R 257 Details of bonding type rmsd hydrogen bonds : bond 0.03377 ( 445) hydrogen bonds : angle 4.08696 ( 1278) SS BOND : bond 0.00418 ( 1) SS BOND : angle 2.11178 ( 2) covalent geometry : bond 0.00252 ( 9275) covalent geometry : angle 0.49962 (12567) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6097.70 seconds wall clock time: 107 minutes 54.80 seconds (6474.80 seconds total)