Starting phenix.real_space_refine on Thu Jan 16 07:08:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f7w_28911/01_2025/8f7w_28911.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f7w_28911/01_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_28911/01_2025/8f7w_28911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f7w_28911/01_2025/8f7w_28911.map" model { file = "/net/cci-nas-00/data/ceres_data/8f7w_28911/01_2025/8f7w_28911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f7w_28911/01_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-5571/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: 5.43, 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: 2.58 Conformation dependent library (CDL) restraints added in 1.1 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: 1.02 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: 2.71 Time building geometry restraints manager: 2.91 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: 0.800 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: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.430 Find NCS groups from input model: 0.120 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.960 ------------------------------------------------------------------------------- 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= 0.255 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 to be fit. rotamer outliers: 1 poor density : 239 time to evaluate : 0.908 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: 0.2357 time to fit residues: 75.0678 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 : 0.943 ------------------------------------------------------------------------------- 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 = 0.140063 restraints weight = 10371.119| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.35 r_work: 0.3235 rms_B_bonded: 3.09 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 9275 Z= 0.431 Angle : 0.669 10.103 12567 Z= 0.351 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 *********************** 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 : 1.082 Fit side-chains revert: symmetry clash REVERT: R 297 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7117 (mt-10) REVERT: A 232 LEU cc_start: 0.8010 (mt) cc_final: 0.7642 (mp) REVERT: B 45 MET cc_start: 0.8750 (mtt) cc_final: 0.8477 (mtp) REVERT: B 46 ARG cc_start: 0.8452 (mtt180) cc_final: 0.7927 (mtp85) REVERT: B 153 ASP cc_start: 0.8300 (m-30) cc_final: 0.7996 (m-30) REVERT: B 247 ASP cc_start: 0.7578 (t0) cc_final: 0.7288 (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: 0.7892 (mt) REVERT: E 46 GLU cc_start: 0.8021 (tt0) cc_final: 0.7714 (tt0) REVERT: E 82 GLN cc_start: 0.8219 (mm110) cc_final: 0.8015 (mm110) REVERT: E 161 ARG cc_start: 0.7438 (tpp-160) cc_final: 0.7190 (tpp-160) outliers start: 29 outliers final: 20 residues processed: 188 average time/residue: 0.2314 time to fit residues: 59.3882 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 : 1.062 ------------------------------------------------------------------------------- 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: 1.9990 chunk 51 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 110 optimal weight: 0.0030 chunk 28 optimal weight: 0.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.184067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.144817 restraints weight = 10605.812| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.32 r_work: 0.3276 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9275 Z= 0.175 Angle : 0.498 6.220 12567 Z= 0.261 Chirality : 0.041 0.206 1442 Planarity : 0.003 0.032 1563 Dihedral : 5.222 41.584 1465 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.03 % Allowed : 9.73 % Favored : 88.25 % 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: 0.22 (0.25), residues: 1129 helix: 1.65 (0.25), residues: 404 sheet: -0.50 (0.28), residues: 300 loop : -0.76 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 99 HIS 0.004 0.001 HIS B 225 PHE 0.012 0.001 PHE R 293 TYR 0.015 0.001 TYR B 59 ARG 0.004 0.000 ARG R 257 *********************** 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 174 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: R 233 PHE cc_start: 0.8113 (m-80) cc_final: 0.7867 (m-80) REVERT: R 297 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7191 (mt-10) REVERT: A 232 LEU cc_start: 0.7976 (mt) cc_final: 0.7611 (mp) REVERT: B 46 ARG cc_start: 0.8394 (mtt180) cc_final: 0.7880 (mtp85) REVERT: B 98 SER cc_start: 0.9046 (m) cc_final: 0.8749 (t) REVERT: B 153 ASP cc_start: 0.8179 (m-30) cc_final: 0.7894 (m-30) REVERT: B 247 ASP cc_start: 0.7653 (t0) cc_final: 0.7362 (t0) REVERT: B 334 SER cc_start: 0.8567 (m) cc_final: 0.8292 (t) REVERT: E 46 GLU cc_start: 0.7932 (tt0) cc_final: 0.7611 (tt0) REVERT: E 82 GLN cc_start: 0.8248 (mm110) cc_final: 0.8027 (mm110) REVERT: E 161 ARG cc_start: 0.7287 (tpp-160) cc_final: 0.7017 (tpp-160) outliers start: 20 outliers final: 12 residues processed: 164 average time/residue: 0.2401 time to fit residues: 53.1152 Evaluate side-chains 161 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 213 VAL 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: 8.9990 chunk 55 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 105 optimal weight: 0.0370 chunk 43 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN E 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.183195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.143439 restraints weight = 10405.338| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.31 r_work: 0.3346 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9275 Z= 0.193 Angle : 0.508 7.725 12567 Z= 0.264 Chirality : 0.042 0.217 1442 Planarity : 0.003 0.039 1563 Dihedral : 5.096 40.415 1465 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.74 % Allowed : 9.93 % Favored : 87.34 % 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: 0.51 (0.25), residues: 1129 helix: 2.00 (0.26), residues: 399 sheet: -0.41 (0.28), residues: 302 loop : -0.62 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 *********************** 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 185 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: R 233 PHE cc_start: 0.8164 (m-80) cc_final: 0.7937 (m-80) REVERT: R 297 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7222 (mt-10) REVERT: A 232 LEU cc_start: 0.7898 (mt) cc_final: 0.7489 (mp) REVERT: A 329 THR cc_start: 0.7432 (OUTLIER) cc_final: 0.7107 (p) REVERT: B 46 ARG cc_start: 0.8397 (mtt180) cc_final: 0.7882 (mtp85) REVERT: B 98 SER cc_start: 0.9068 (m) cc_final: 0.8780 (t) REVERT: B 153 ASP cc_start: 0.8189 (m-30) cc_final: 0.7927 (m-30) REVERT: B 247 ASP cc_start: 0.7718 (t0) cc_final: 0.7457 (t0) REVERT: B 334 SER cc_start: 0.8544 (m) cc_final: 0.8255 (t) REVERT: C 41 CYS cc_start: 0.8180 (m) cc_final: 0.7925 (m) REVERT: E 46 GLU cc_start: 0.8058 (tt0) cc_final: 0.7777 (tt0) REVERT: E 82 GLN cc_start: 0.8222 (mm110) cc_final: 0.7982 (mm110) REVERT: E 158 ILE cc_start: 0.7026 (OUTLIER) cc_final: 0.6653 (pt) REVERT: E 161 ARG cc_start: 0.7333 (tpp-160) cc_final: 0.7053 (tpp-160) outliers start: 27 outliers final: 24 residues processed: 174 average time/residue: 0.2365 time to fit residues: 55.8847 Evaluate side-chains 180 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 243 ILE Chi-restraints excluded: chain R residue 266 ASP Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 336 ASN Chi-restraints excluded: chain A residue 184 ILE 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 32 GLN 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 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 24 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.181791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.141321 restraints weight = 10642.001| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.44 r_work: 0.3311 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9275 Z= 0.156 Angle : 0.480 8.071 12567 Z= 0.249 Chirality : 0.041 0.220 1442 Planarity : 0.003 0.035 1563 Dihedral : 4.907 39.399 1465 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.94 % Allowed : 11.04 % 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: 0.80 (0.25), residues: 1129 helix: 2.21 (0.26), residues: 406 sheet: -0.22 (0.29), residues: 300 loop : -0.48 (0.30), residues: 423 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 0.010 0.001 PHE A 189 TYR 0.012 0.001 TYR R 140 ARG 0.004 0.000 ARG B 197 *********************** 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 186 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: R 91 LYS cc_start: 0.7522 (mptt) cc_final: 0.7227 (mmtt) REVERT: R 233 PHE cc_start: 0.8155 (m-80) cc_final: 0.7930 (m-80) REVERT: R 297 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7137 (mt-10) REVERT: P 211 PHE cc_start: 0.8623 (m-80) cc_final: 0.8358 (m-80) REVERT: A 232 LEU cc_start: 0.7775 (mt) cc_final: 0.7304 (mp) REVERT: A 306 GLN cc_start: 0.8084 (mt0) cc_final: 0.7783 (mt0) REVERT: A 329 THR cc_start: 0.7359 (OUTLIER) cc_final: 0.7054 (p) REVERT: B 46 ARG cc_start: 0.8328 (mtt180) cc_final: 0.7756 (mtp85) REVERT: B 98 SER cc_start: 0.9022 (m) cc_final: 0.8723 (t) REVERT: B 153 ASP cc_start: 0.8012 (m-30) cc_final: 0.7729 (m-30) REVERT: B 247 ASP cc_start: 0.7800 (t0) cc_final: 0.7542 (t0) REVERT: C 41 CYS cc_start: 0.8179 (m) cc_final: 0.7936 (m) REVERT: E 46 GLU cc_start: 0.7978 (tt0) cc_final: 0.7564 (mt-10) REVERT: E 161 ARG cc_start: 0.7309 (tpp-160) cc_final: 0.6989 (tpp-160) outliers start: 29 outliers final: 21 residues processed: 176 average time/residue: 0.2238 time to fit residues: 54.1082 Evaluate side-chains 175 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 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 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 234 PHE Chi-restraints excluded: chain B residue 243 THR 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: 1.9990 chunk 77 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 33 optimal weight: 0.0040 chunk 36 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 122 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 = 0.4140 r_free = 0.4140 target = 0.182214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.141727 restraints weight = 10566.679| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.42 r_work: 0.3365 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9275 Z= 0.143 Angle : 0.474 8.808 12567 Z= 0.244 Chirality : 0.041 0.223 1442 Planarity : 0.003 0.034 1563 Dihedral : 4.769 38.124 1465 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.03 % Allowed : 12.26 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.25), residues: 1129 helix: 2.39 (0.26), residues: 405 sheet: -0.02 (0.29), residues: 284 loop : -0.47 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 221 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 *********************** 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 172 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 1.110 Fit side-chains revert: symmetry clash REVERT: R 91 LYS cc_start: 0.7523 (mptt) cc_final: 0.7188 (mmtt) REVERT: R 233 PHE cc_start: 0.8227 (m-80) cc_final: 0.7995 (m-80) REVERT: A 232 LEU cc_start: 0.7834 (mt) cc_final: 0.7384 (mp) REVERT: A 329 THR cc_start: 0.7391 (OUTLIER) cc_final: 0.7064 (p) REVERT: B 46 ARG cc_start: 0.8370 (mtt180) cc_final: 0.7814 (mtp85) REVERT: B 98 SER cc_start: 0.9030 (m) cc_final: 0.8779 (t) REVERT: B 153 ASP cc_start: 0.8074 (m-30) cc_final: 0.7816 (m-30) REVERT: B 247 ASP cc_start: 0.7939 (t0) cc_final: 0.7686 (t0) REVERT: C 42 GLU cc_start: 0.8212 (mt-10) cc_final: 0.8009 (mt-10) REVERT: E 46 GLU cc_start: 0.8000 (tt0) cc_final: 0.7674 (mt-10) REVERT: E 161 ARG cc_start: 0.7332 (tpp-160) cc_final: 0.7021 (tpp-160) outliers start: 20 outliers final: 18 residues processed: 165 average time/residue: 0.2547 time to fit residues: 56.6577 Evaluate side-chains 167 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 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 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 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 91 THR 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: 0.9990 chunk 97 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 98 optimal weight: 0.0970 chunk 102 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 101 optimal weight: 0.0030 overall best weight: 1.3992 ------------------------------------------------------------------------------- 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 E 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.181914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.141502 restraints weight = 10618.280| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.59 r_work: 0.3246 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9275 Z= 0.213 Angle : 0.512 9.336 12567 Z= 0.262 Chirality : 0.042 0.226 1442 Planarity : 0.003 0.034 1563 Dihedral : 4.923 36.921 1465 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.84 % Allowed : 11.45 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.25), residues: 1129 helix: 2.31 (0.26), residues: 405 sheet: -0.16 (0.28), residues: 296 loop : -0.35 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 221 HIS 0.004 0.001 HIS B 225 PHE 0.014 0.001 PHE A 267 TYR 0.015 0.001 TYR B 59 ARG 0.007 0.000 ARG B 134 *********************** 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 193 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.939 Fit side-chains REVERT: R 233 PHE cc_start: 0.8128 (m-80) cc_final: 0.7893 (m-80) REVERT: A 232 LEU cc_start: 0.7887 (mt) cc_final: 0.7458 (mp) REVERT: A 315 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7367 (m-30) REVERT: A 329 THR cc_start: 0.7313 (OUTLIER) cc_final: 0.7018 (p) REVERT: B 46 ARG cc_start: 0.8163 (mtt180) cc_final: 0.7689 (mtp85) REVERT: B 98 SER cc_start: 0.9001 (m) cc_final: 0.8751 (t) REVERT: B 153 ASP cc_start: 0.7958 (m-30) cc_final: 0.7620 (m-30) REVERT: B 247 ASP cc_start: 0.7859 (t0) cc_final: 0.7574 (t0) REVERT: C 42 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7846 (mt-10) REVERT: E 46 GLU cc_start: 0.7826 (tt0) cc_final: 0.7512 (mt-10) REVERT: E 161 ARG cc_start: 0.7310 (tpp-160) cc_final: 0.6996 (tpp-160) outliers start: 28 outliers final: 23 residues processed: 181 average time/residue: 0.2292 time to fit residues: 55.8529 Evaluate side-chains 180 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 228 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 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 65 THR 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 72 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.3980 chunk 48 optimal weight: 0.4980 chunk 91 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.184260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.144062 restraints weight = 10704.802| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.32 r_work: 0.3476 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3897 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= 0.145 Angle : 0.486 9.889 12567 Z= 0.250 Chirality : 0.041 0.222 1442 Planarity : 0.003 0.033 1563 Dihedral : 4.791 36.173 1465 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.43 % Allowed : 12.16 % 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: 1.08 (0.25), residues: 1129 helix: 2.48 (0.26), residues: 405 sheet: -0.04 (0.29), residues: 286 loop : -0.40 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 258 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 *********************** 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 183 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 1.031 Fit side-chains REVERT: R 233 PHE cc_start: 0.8184 (m-80) cc_final: 0.7939 (m-80) REVERT: A 306 GLN cc_start: 0.8180 (mt0) cc_final: 0.7815 (mt0) REVERT: A 315 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7370 (m-30) REVERT: A 329 THR cc_start: 0.7301 (OUTLIER) cc_final: 0.7002 (p) REVERT: B 46 ARG cc_start: 0.8162 (mtt180) cc_final: 0.7826 (mtp85) REVERT: B 153 ASP cc_start: 0.7851 (m-30) cc_final: 0.7638 (m-30) REVERT: B 213 VAL cc_start: 0.8850 (OUTLIER) cc_final: 0.8510 (m) REVERT: B 247 ASP cc_start: 0.7853 (t0) cc_final: 0.7576 (t0) REVERT: C 42 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7918 (mt-10) REVERT: E 46 GLU cc_start: 0.7794 (tt0) cc_final: 0.7582 (mt-10) REVERT: E 161 ARG cc_start: 0.7297 (tpp-160) cc_final: 0.7038 (tpp-160) outliers start: 24 outliers final: 19 residues processed: 173 average time/residue: 0.2558 time to fit residues: 60.0381 Evaluate side-chains 171 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 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 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 91 THR Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 239 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.7246 > 50: distance: 110 - 169: 12.616 distance: 113 - 166: 30.910 distance: 142 - 144: 6.194 distance: 144 - 145: 3.832 distance: 145 - 146: 24.011 distance: 145 - 148: 17.155 distance: 146 - 147: 18.952 distance: 146 - 153: 48.747 distance: 148 - 149: 22.700 distance: 149 - 150: 5.066 distance: 150 - 151: 11.126 distance: 150 - 152: 11.019 distance: 153 - 154: 33.641 distance: 154 - 155: 28.698 distance: 154 - 157: 12.049 distance: 155 - 156: 34.904 distance: 155 - 159: 16.169 distance: 157 - 158: 17.389 distance: 159 - 160: 30.427 distance: 159 - 165: 33.932 distance: 160 - 161: 36.980 distance: 160 - 163: 26.692 distance: 161 - 162: 11.708 distance: 161 - 166: 39.577 distance: 163 - 164: 32.793 distance: 166 - 167: 40.856 distance: 167 - 168: 25.134 distance: 167 - 170: 37.735 distance: 168 - 169: 19.095 distance: 168 - 175: 18.197 distance: 170 - 171: 4.310 distance: 171 - 172: 15.932 distance: 172 - 173: 6.755 distance: 172 - 174: 17.260 distance: 175 - 176: 19.781 distance: 176 - 177: 25.887 distance: 176 - 179: 25.030 distance: 177 - 178: 8.786 distance: 177 - 183: 25.294 distance: 179 - 180: 26.003 distance: 180 - 181: 11.932 distance: 180 - 182: 8.609 distance: 183 - 184: 42.447 distance: 184 - 185: 43.895 distance: 184 - 187: 37.919 distance: 185 - 186: 44.995 distance: 185 - 191: 32.967 distance: 187 - 188: 45.077 distance: 188 - 189: 7.628 distance: 188 - 190: 18.447 distance: 191 - 192: 22.396 distance: 192 - 193: 37.965 distance: 192 - 195: 24.100 distance: 193 - 194: 37.365 distance: 193 - 199: 43.177 distance: 195 - 196: 21.541 distance: 195 - 197: 21.937 distance: 196 - 198: 19.379 distance: 199 - 200: 18.812 distance: 199 - 239: 23.693 distance: 200 - 201: 25.346 distance: 200 - 203: 21.409 distance: 201 - 202: 6.505 distance: 201 - 211: 26.745 distance: 202 - 236: 18.100 distance: 203 - 204: 10.034 distance: 204 - 205: 21.184 distance: 204 - 206: 7.660 distance: 205 - 207: 4.046 distance: 206 - 208: 10.820 distance: 207 - 209: 18.387 distance: 208 - 209: 12.519 distance: 209 - 210: 29.721 distance: 211 - 212: 11.977 distance: 212 - 213: 11.080 distance: 212 - 215: 14.680 distance: 213 - 214: 12.627 distance: 213 - 222: 13.277 distance: 215 - 216: 8.375 distance: 216 - 217: 8.737 distance: 217 - 218: 11.327 distance: 218 - 219: 8.517 distance: 219 - 220: 9.469 distance: 219 - 221: 14.557 distance: 222 - 223: 23.050 distance: 223 - 224: 6.146 distance: 223 - 226: 15.595 distance: 224 - 225: 14.630 distance: 224 - 230: 9.544 distance: 226 - 227: 8.547 distance: 227 - 228: 8.618 distance: 228 - 229: 3.661